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Du SW, Komirisetty R, Lewandowski D, Choi EH, Panas D, Suh S, Tabaka M, Radu RA, Palczewski K. Conditional deletion of miR-204 and miR-211 in murine retinal pigment epithelium results in retinal degeneration. J Biol Chem 2024:107344. [PMID: 38705389 DOI: 10.1016/j.jbc.2024.107344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/18/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024] Open
Abstract
MicroRNAs (miRs) are short, evolutionarily conserved non-coding RNAs that canonically downregulate expression of target genes. The miR family composed of miR-204 and miR-211 is among the most highly expressed in the retinal pigment epithelium (RPE) in both mouse and human, and also retains high sequence identity. To assess the role of this miR family in the developed mouse eye, we generated two floxed conditional knockout mouse lines crossed to the RPE65-ERT2-Cre driver mouse line to perform an RPE-specific conditional knockout of this miR family in adult mice. After Cre-mediated deletion, we observed retinal structural changes by optical coherence tomography; dysfunction and loss of photoreceptors by retinal imaging; and retinal inflammation marked by subretinal infiltration of immune cells by imaging and immunostaining. Single-cell RNA sequencing of diseased RPE and retinas showed potential miR-regulated target genes, as well as changes in non-coding RNAs in the RPE, rod photoreceptors, and Müller glia. This work thus highlights the role of miR-204 and miR-211 in maintaining RPE function and how the loss of miRs in the RPE exerts effects on the neural retina, leading to inflammation and retinal degeneration.
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Affiliation(s)
- Samuel W Du
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, Irvine, CA, 92697, USA; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Ravikiran Komirisetty
- Department of Ophthalmology and UCLA Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Dominik Lewandowski
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Elliot H Choi
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Damian Panas
- International Centre for Translational Eye Research, Warsaw 01224, Poland; Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw 01224, Poland
| | - Susie Suh
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw 01224, Poland; Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw 01224, Poland
| | - Roxana A Radu
- Department of Ophthalmology and UCLA Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, Irvine, CA, 92697, USA; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA; Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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2
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Lewandowski D, Gao F, Imanishi S, Tworak A, Bassetto M, Dong Z, Pinto AFM, Tabaka M, Kiser PD, Imanishi Y, Skowronska-Krawczyk D, Palczewski K. Restoring retinal polyunsaturated fatty acid balance and retina function by targeting ceramide in AdipoR1 deficient mice. J Biol Chem 2024:107291. [PMID: 38636661 DOI: 10.1016/j.jbc.2024.107291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/30/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Mutations in the adiponectin receptor 1 gene (AdipoR1) lead to retinitis pigmentosa and are associated with age-related macular degeneration (AMD). This study explores the effects of AdipoR1 gene deficiency in mice, revealing a striking decline in ω3 polyunsaturated fatty acids (PUFA), an increase in ω6 FAs, and elevated ceramides in the retina. The AdipoR1 deficiency impairs peroxisome proliferator-activated receptor α (PPARα) signaling, which is crucial for FA metabolism, particularly affecting proteins associated with FA transport and oxidation in the retina and retinal pigmented epithelium (RPE). Our lipidomic and proteomic analyses indicate changes that could affect membrane composition and viscosity through altered ω3 PUFA transport and synthesis, suggesting a potential influence of AdipoR1 on these properties. Furthermore, we noted a reduction in the Bardet-Biedl syndrome (BBS) proteins, which are crucial for forming and maintaining photoreceptor outer segments that are PUFA-enriched ciliary structures. Diminution in BBS-proteins content combined with our electron microscopic observations raises the possibility that AdipoR1 deficiency might impair ciliary function. Treatment with inhibitors of ceramide synthesis led to substantial elevation of ω3 LC-PUFAs, alleviating photoreceptor degeneration and improving retinal function. These results serve as the proof of concept for a ceramide-targeted strategy to treat retinopathies linked to PUFA deficiency, including AMD.
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Affiliation(s)
- Dominik Lewandowski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA.
| | - Fangyuan Gao
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Sanae Imanishi
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Aleksander Tworak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Marco Bassetto
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Zhiqian Dong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Marcin Tabaka
- International Centre for Translational Eye Research, 01-230 Warsaw, Poland; Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA; Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA; Department of Clinical Pharmacy Practice, University of California, Irvine, CA 92697; Research Service, Veterans Affairs Long Beach Healthcare System, Long Beach, CA, 90822
| | - Yoshikazu Imanishi
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Dorota Skowronska-Krawczyk
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA; Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA; Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA; Department of Chemistry, and Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.
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3
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Engfer ZJ, Lewandowski D, Dong Z, Palczewska G, Zhang J, Kordecka K, Płaczkiewicz J, Panas D, Foik AT, Tabaka M, Palczewski K. Distinct mouse models of Stargardt disease display differences in pharmacological targeting of ceramides and inflammatory responses. Proc Natl Acad Sci U S A 2023; 120:e2314698120. [PMID: 38064509 PMCID: PMC10723050 DOI: 10.1073/pnas.2314698120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/25/2023] [Indexed: 12/17/2023] Open
Abstract
Mutations in many visual cycle enzymes in photoreceptors and retinal pigment epithelium (RPE) cells can lead to the chronic accumulation of toxic retinoid byproducts, which poison photoreceptors and the underlying RPE if left unchecked. Without a functional ATP-binding cassette, sub-family A, member 4 (ABCA4), there is an elevation of all-trans-retinal and prolonged buildup of all-trans-retinal adducts, resulting in a retinal degenerative disease known as Stargardt-1 disease. Even in this monogenic disorder, there is significant heterogeneity in the time to onset of symptoms among patients. Using a combination of molecular techniques, we studied Abca4 knockout (simulating human noncoding disease variants) and Abca4 knock-in mice (simulating human misfolded, catalytically inactive protein variants), which serve as models for Stargardt-1 disease. We compared the two strains to ascertain whether they exhibit differential responses to agents that affect cytokine signaling and/or ceramide metabolism, as alterations in either of these pathways can exacerbate retinal degenerative phenotypes. We found different degrees of responsiveness to maraviroc, a known immunomodulatory CCR5 antagonist, and to the ceramide-lowering agent AdipoRon, an agonist of the ADIPOR1 and ADIPOR2 receptors. The two strains also display different degrees of transcriptional deviation from matched WT controls. Our phenotypic comparison of the two distinct Abca4 mutant-mouse models sheds light on potential therapeutic avenues previously unexplored in the treatment of Stargardt disease and provides a surrogate assay for assessing the effectiveness for genome editing.
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Affiliation(s)
- Zachary J. Engfer
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
| | - Dominik Lewandowski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
| | - Zhiqian Dong
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
| | - Grazyna Palczewska
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
| | - Jianye Zhang
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
| | - Katarzyna Kordecka
- Ophthalmic Biology Group, International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Jagoda Płaczkiewicz
- Ophthalmic Biology Group, International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Damian Panas
- International Centre for Translational Eye Research, Warsaw01-224, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Andrzej T. Foik
- Ophthalmic Biology Group, International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw01-224, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
- Department of Chemistry, University of California, Irvine, CA92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697
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4
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De Jonghe J, Kaminski TS, Morse DB, Tabaka M, Ellermann AL, Kohler TN, Amadei G, Handford CE, Findlay GM, Zernicka-Goetz M, Teichmann SA, Hollfelder F. spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content. Nat Commun 2023; 14:4788. [PMID: 37553326 PMCID: PMC10409775 DOI: 10.1038/s41467-023-40322-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RNA capture efficiency is lower. These drawbacks stem from the lack of strategies to enrich for high-quality material or specific cell types at the moment of cell encapsulation and the absence of implementable multi-step enzymatic processes that increase capture. Here we alleviate both bottlenecks using fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei, fixed cells or target cell types and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half. We harness these properties to deliver a high-quality molecular atlas of mouse brain development, despite starting with highly damaged input material, and provide an atlas of nascent RNA transcription during mouse organogenesis. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.
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Affiliation(s)
- Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - David B Morse
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Gianluca Amadei
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte E Handford
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | | | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, USA
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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5
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C. Luu J, Saadane A, Leinonen H, H. Choi E, Gao F, Lewandowski D, Halabi M, L. Sander C, Wu A, Wang JM, Singh R, Gao S, Lessieur EM, Dong Z, Palczewska G, Mullins RF, Peachey NS, Kiser PD, Tabaka M, Kern TS, Palczewski K. Stress resilience-enhancing drugs preserve tissue structure and function in degenerating retina via phosphodiesterase inhibition. Proc Natl Acad Sci U S A 2023; 120:e2221045120. [PMID: 37126699 PMCID: PMC10175720 DOI: 10.1073/pnas.2221045120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/02/2023] [Indexed: 05/03/2023] Open
Abstract
Chronic, progressive retinal diseases, such as age-related macular degeneration (AMD), diabetic retinopathy, and retinitis pigmentosa, arise from genetic and environmental perturbations of cellular and tissue homeostasis. These disruptions accumulate with repeated exposures to stress over time, leading to progressive visual impairment and, in many cases, legal blindness. Despite decades of research, therapeutic options for the millions of patients suffering from these disorders remain severely limited, especially for treating earlier stages of pathogenesis when the opportunity to preserve the retinal structure and visual function is greatest. To address this urgent, unmet medical need, we employed a systems pharmacology platform for therapeutic development. Through integrative single-cell transcriptomics, proteomics, and phosphoproteomics, we identified universal molecular mechanisms across distinct models of age-related and inherited retinal degenerations, characterized by impaired physiological resilience to stress. Here, we report that selective, targeted pharmacological inhibition of cyclic nucleotide phosphodiesterases (PDEs), which serve as critical regulatory nodes that modulate intracellular second messenger signaling pathways, stabilized the transcriptome, proteome, and phosphoproteome through downstream activation of protective mechanisms coupled with synergistic inhibition of degenerative processes. This therapeutic intervention enhanced resilience to acute and chronic forms of stress in the degenerating retina, thus preserving tissue structure and function across various models of age-related and inherited retinal disease. Taken together, these findings exemplify a systems pharmacology approach to drug discovery and development, revealing a new class of therapeutics with potential clinical utility in the treatment or prevention of the most common causes of blindness.
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Affiliation(s)
- Jennings C. Luu
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Aicha Saadane
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Henri Leinonen
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
- Department of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio70211, Finland
| | - Elliot H. Choi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Fangyuan Gao
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Dominik Lewandowski
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Maximilian Halabi
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Christopher L. Sander
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Arum Wu
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Jacob M. Wang
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH44195
| | - Rupesh Singh
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH44195
| | - Songqi Gao
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Emma M. Lessieur
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Zhiqian Dong
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Grazyna Palczewska
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Robert F. Mullins
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA52242
| | - Neal S. Peachey
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH44195
- Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH44106
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH44195
| | - Philip D. Kiser
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
- Department of Physiology & Biophysics, School of Medicine, University of California-Irvine, Irvine, CA92697
- Research Service, VA Long Beach Healthcare System, Long Beach, CA90822
- Department of Clinical Pharmacy Practice, University of California-Irvine, Irvine, CA92697
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw01224, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01224, Poland
| | - Timothy S. Kern
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
| | - Krzysztof Palczewski
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA92697
- Department of Physiology & Biophysics, School of Medicine, University of California-Irvine, Irvine, CA92697
- International Centre for Translational Eye Research, Warsaw01224, Poland
- Department of Chemistry, University of California-Irvine, Irvine, CA92697
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA92697
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6
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Tang R, Acharya N, Subramanian A, Purohit V, Tabaka M, Hou Y, He D, Dixon KO, Lambden C, Xia J, Rozenblatt-Rosen O, Sobel RA, Wang C, Regev A, Anderson AC, Kuchroo VK. Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function. Sci Immunol 2022; 7:eabm0631. [PMID: 35275752 PMCID: PMC9273260 DOI: 10.1126/sciimmunol.abm0631] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Dendritic cells (DCs) sense environmental cues and adopt either an immune-stimulatory or regulatory phenotype, thereby fine-tuning immune responses. Identifying endogenous regulators that determine DC function can thus inform the development of therapeutic strategies for modulating the immune response in different disease contexts. Tim-3 plays an important role in regulating immune responses by inhibiting the activation status and the T cell priming ability of DC in the setting of cancer. Bat3 is an adaptor protein that binds to the tail of Tim-3; therefore, we studied its role in regulating the functional status of DCs. In murine models of autoimmunity (experimental autoimmune encephalomyelitis) and cancer (MC38-OVA-implanted tumor), lack of Bat3 expression in DCs alters the T cell compartment-it decreases TH1, TH17 and cytotoxic effector cells, increases regulatory T cells, and exhausted CD8+ tumor-infiltrating lymphocytes, resulting in the attenuation of autoimmunity and acceleration of tumor growth. We found that Bat3 expression levels were differentially regulated by activating versus inhibitory stimuli in DCs, indicating a role for Bat3 in the functional calibration of DC phenotypes. Mechanistically, loss of Bat3 in DCs led to hyperactive unfolded protein response and redirected acetyl-coenzyme A to increase cell intrinsic steroidogenesis. The enhanced steroidogenesis in Bat3-deficient DC suppressed T cell response in a paracrine manner. Our findings identified Bat3 as an endogenous regulator of DC function, which has implications for DC-based immunotherapies.
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Affiliation(s)
- Ruihan Tang
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nandini Acharya
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ayshwarya Subramanian
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vinee Purohit
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yu Hou
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Danyang He
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Karen O. Dixon
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Connor Lambden
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Junrong Xia
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Chao Wang
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ana C. Anderson
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Vijay K. Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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7
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Lewandowski D, Foik AT, Smidak R, Choi EH, Zhang J, Hoang T, Tworak A, Suh S, Leinonen H, Dong Z, Pinto AF, Tom E, Luu JC, Lee JY, Ma X, Bieberich E, Blackshaw S, Saghatelian A, Lyon DC, Skowronska-Krawczyk D, Tabaka M, Palczewski K. Inhibition of ceramide accumulation in AdipoR1-/- mice increases photoreceptor survival and improves vision. JCI Insight 2022; 7:156301. [PMID: 35015730 PMCID: PMC8876453 DOI: 10.1172/jci.insight.156301] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Adiponectin receptor 1 (ADIPOR1) is a lipid and glucose metabolism regulator that possesses intrinsic ceramidase activity. Mutations of the ADIPOR1 gene have been associated with nonsyndromic and syndromic retinitis pigmentosa. Here, we show that the absence of AdipoR1 in mice leads to progressive photoreceptor degeneration, significant reduction of electroretinogram amplitudes, decreased retinoid content in the retina, and reduced cone opsin expression. Single-cell RNA-Seq results indicate that ADIPOR1 encoded the most abundantly expressed ceramidase in mice and one of the 2 most highly expressed ceramidases in the human retina, next to acid ceramidase ASAH1. We discovered an accumulation of ceramides in the AdipoR1–/– retina, likely due to insufficient ceramidase activity for healthy retina function, resulting in photoreceptor death. Combined treatment with desipramine/L-cycloserine (DC) lowered ceramide levels and exerted a protective effect on photoreceptors in AdipoR1–/– mice. Moreover, we observed improvement in cone-mediated retinal function in the DC-treated animals. Lastly, we found that prolonged DC treatment corrected the electrical responses of the primary visual cortex to visual stimuli, approaching near-normal levels for some parameters. These results highlight the importance of ADIPOR1 ceramidase in the retina and show that pharmacological inhibition of ceramide generation can provide a therapeutic strategy for ADIPOR1-related retinopathy.
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Affiliation(s)
- Dominik Lewandowski
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Andrzej T Foik
- International Center for Translational Eye Research, Institute of Physical Chemistry PAS, Warsaw, Poland
| | - Roman Smidak
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Elliot H Choi
- Department of Pharmacology, Case Western Reserve University, Cleveland, United States of America
| | - Jianye Zhang
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Aleksander Tworak
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Susie Suh
- Department of Pharmacology, Case Western Reserve University, Cleveland, United States of America
| | - Henri Leinonen
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Zhiqian Dong
- Department of Medical Devices, Polgenix Inc., Cleveland, United States of America
| | - Antonio Fm Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, United States of America
| | - Emily Tom
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Jennings C Luu
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Joan Y Lee
- MetroHealth Medical Center, Case Western Reserve University, Cleveland, United States of America
| | - Xiuli Ma
- Department of Medical Devices, Polgenix Inc, Cleveland, United States of America
| | - Erhard Bieberich
- Department of Physiology, University of Kentucky, Lexington, United States of America
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, John Hopkins School of Medicine, Baltimore, United States of America
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, United States of America
| | - David C Lyon
- Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, United States of America
| | | | - Marcin Tabaka
- International Center for Translational Eye Research, Institute of Physical Chemistry PAS, Warsaw, Poland
| | - Krzysztof Palczewski
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
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8
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Oren Y, Tsabar M, Cuoco MS, Amir-Zilberstein L, Cabanos HF, Hütter JC, Hu B, Thakore PI, Tabaka M, Fulco CP, Colgan W, Cuevas BM, Hurvitz SA, Slamon DJ, Deik A, Pierce KA, Clish C, Hata AN, Zaganjor E, Lahav G, Politi K, Brugge JS, Regev A. Cycling cancer persister cells arise from lineages with distinct programs. Nature 2021; 596:576-582. [PMID: 34381210 PMCID: PMC9209846 DOI: 10.1038/s41586-021-03796-6] [Citation(s) in RCA: 194] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/02/2021] [Indexed: 02/07/2023]
Abstract
Non-genetic mechanisms have recently emerged as important drivers of cancer therapy failure1, where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment2. Although most cancer persisters remain arrested in the presence of the drug, a rare subset can re-enter the cell cycle under constitutive drug treatment. Little is known about the non-genetic mechanisms that enable cancer persisters to maintain proliferative capacity in the presence of drugs. To study this rare, transiently resistant, proliferative persister population, we developed Watermelon, a high-complexity expressed barcode lentiviral library for simultaneous tracing of each cell's clonal origin and proliferative and transcriptional states. Here we show that cycling and non-cycling persisters arise from different cell lineages with distinct transcriptional and metabolic programs. Upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation are associated with persister proliferative capacity across multiple cancer types. Impeding oxidative stress or metabolic reprogramming alters the fraction of cycling persisters. In human tumours, programs associated with cycling persisters are induced in minimal residual disease in response to multiple targeted therapies. The Watermelon system enabled the identification of rare persister lineages that are preferentially poised to proliferate under drug pressure, thus exposing new vulnerabilities that can be targeted to delay or even prevent disease recurrence.
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Affiliation(s)
- Yaara Oren
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, USA
| | - Michael Tsabar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Systems Biology, Harvard Medical School, Boston, MA, USA,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael S. Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Heidie F. Cabanos
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA,Departments of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jan-Christian Hütter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bomiao Hu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Pratiksha I. Thakore
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Current address: Genentech, South San Francisco, CA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Current address: Bristol Myers Squibb, Cambridge, MA, USA
| | | | - Brandon M. Cuevas
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara A. Hurvitz
- David Geffen School of Medicine, University of California, Los Angeles, Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Dennis J. Slamon
- David Geffen School of Medicine, University of California, Los Angeles, Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Amy Deik
- Metabolomics Platform, Broad Institute, Cambridge, MA, USA
| | | | - Clary Clish
- Metabolomics Platform, Broad Institute, Cambridge, MA, USA
| | - Aaron N. Hata
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA,Departments of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elma Zaganjor
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Katerina Politi
- Departments of Pathology (Section of Medical Oncology), Yale School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | - Joan S. Brugge
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, USA,Ludwig Center at Harvard
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Genentech, South San Francisco, CA, USA.
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9
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Dixon KO, Tabaka M, Schramm MA, Xiao S, Tang R, Dionne D, Anderson AC, Rozenblatt-Rosen O, Regev A, Kuchroo VK. TIM-3 restrains anti-tumour immunity by regulating inflammasome activation. Nature 2021; 595:101-106. [PMID: 34108686 PMCID: PMC8627694 DOI: 10.1038/s41586-021-03626-9] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023]
Abstract
T cell immunoglobulin and mucin-containing molecule 3 (TIM-3), first identified as a molecule expressed on interferon-γ producing T cells1, is emerging as an important immune-checkpoint molecule, with therapeutic blockade of TIM-3 being investigated in multiple human malignancies. Expression of TIM-3 on CD8+ T cells in the tumour microenvironment is considered a cardinal sign of T cell dysfunction; however, TIM-3 is also expressed on several other types of immune cell, confounding interpretation of results following blockade using anti-TIM-3 monoclonal antibodies. Here, using conditional knockouts of TIM-3 together with single-cell RNA sequencing, we demonstrate the singular importance of TIM-3 on dendritic cells (DCs), whereby loss of TIM-3 on DCs-but not on CD4+ or CD8+ T cells-promotes strong anti-tumour immunity. Loss of TIM-3 prevented DCs from expressing a regulatory program and facilitated the maintenance of CD8+ effector and stem-like T cells. Conditional deletion of TIM-3 in DCs led to increased accumulation of reactive oxygen species resulting in NLRP3 inflammasome activation. Inhibition of inflammasome activation, or downstream effector cytokines interleukin-1β (IL-1β) and IL-18, completely abrogated the protective anti-tumour immunity observed with TIM-3 deletion in DCs. Together, our findings reveal an important role for TIM-3 in regulating DC function and underscore the potential of TIM-3 blockade in promoting anti-tumour immunity by regulating inflammasome activation.
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Affiliation(s)
- Karen O Dixon
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Markus A Schramm
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Department of Rheumatology and Clinical Immunology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sheng Xiao
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Celsius Therapeutics, Cambridge, MA, USA
| | - Ruihan Tang
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Koch Institute and Ludwig Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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10
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Bao EL, Nandakumar SK, Liao X, Bick AG, Karjalainen J, Tabaka M, Gan OI, Havulinna AS, Kiiskinen TTJ, Lareau CA, de Lapuente Portilla AL, Li B, Emdin C, Codd V, Nelson CP, Walker CJ, Churchhouse C, de la Chapelle A, Klein DE, Nilsson B, Wilson PWF, Cho K, Pyarajan S, Gaziano JM, Samani NJ, Regev A, Palotie A, Neale BM, Dick JE, Natarajan P, O'Donnell CJ, Daly MJ, Milyavsky M, Kathiresan S, Sankaran VG. Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells. Nature 2020; 586:769-775. [PMID: 33057200 PMCID: PMC7606745 DOI: 10.1038/s41586-020-2786-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/03/2020] [Indexed: 12/17/2022]
Abstract
Myeloproliferative neoplasms (MPNs) are blood cancers that are characterized by the excessive production of mature myeloid cells and arise from the acquisition of somatic driver mutations in haematopoietic stem cells (HSCs). Epidemiological studies indicate a substantial heritable component of MPNs that is among the highest known for cancers1. However, only a limited number of genetic risk loci have been identified, and the underlying biological mechanisms that lead to the acquisition of MPNs remain unclear. Here, by conducting a large-scale genome-wide association study (3,797 cases and 1,152,977 controls), we identify 17 MPN risk loci (P < 5.0 × 10-8), 7 of which have not been previously reported. We find that there is a shared genetic architecture between MPN risk and several haematopoietic traits from distinct lineages; that there is an enrichment for MPN risk variants within accessible chromatin of HSCs; and that increased MPN risk is associated with longer telomere length in leukocytes and other clonal haematopoietic states-collectively suggesting that MPN risk is associated with the function and self-renewal of HSCs. We use gene mapping to identify modulators of HSC biology linked to MPN risk, and show through targeted variant-to-function assays that CHEK2 and GFI1B have roles in altering the function of HSCs to confer disease risk. Overall, our results reveal a previously unappreciated mechanism for inherited MPN risk through the modulation of HSC function.
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Affiliation(s)
- Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaotian Liao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander G Bick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- VA Boston Healthcare, Section of Cardiology, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Marcin Tabaka
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Tuomo T J Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Caleb A Lareau
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | | | - Bo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Connor Emdin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Veryan Codd
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Christopher J Walker
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Albert de la Chapelle
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Daryl E Klein
- Department of Pharmacology, Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, USA
| | - Björn Nilsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Peter W F Wilson
- Atlanta VA Medical Center, Atlanta, GA, USA
- Emory Clinical Cardiovascular Research Institute, Atlanta, GA, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Saiju Pyarajan
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biology, Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aarno Palotie
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare, Section of Cardiology, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Verve Therapeutics, Cambridge, MA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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11
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Li B, Gould J, Yang Y, Sarkizova S, Tabaka M, Ashenberg O, Rosen Y, Slyper M, Kowalczyk MS, Villani AC, Tickle T, Hacohen N, Rozenblatt-Rosen O, Regev A. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Nat Methods 2020; 17:793-798. [PMID: 32719530 PMCID: PMC7437817 DOI: 10.1038/s41592-020-0905-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/18/2020] [Indexed: 11/10/2022]
Abstract
Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. Here we developed Cumulus-a cloud-based framework for analyzing large-scale single-cell and single-nucleus RNA sequencing datasets. Cumulus combines the power of cloud computing with improvements in algorithm and implementation to achieve high scalability, low cost, user-friendliness and integrated support for a comprehensive set of features. We benchmark Cumulus on the Human Cell Atlas Census of Immune Cells dataset of bone marrow cells and show that it substantially improves efficiency over conventional frameworks, while maintaining or improving the quality of results, enabling large-scale studies.
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Affiliation(s)
- Bo Li
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Monika S Kowalczyk
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Timothy Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nir Hacohen
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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12
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Lavaert M, Liang KL, Vandamme N, Park JE, Roels J, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Vandekerckhove B, Leclercq G, Regev A, Van Vlierberghe P, Guilliams M, Teichmann SA, Saeys Y, Taghon T. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Immunity 2020; 52:1088-1104.e6. [PMID: 32304633 DOI: 10.1016/j.immuni.2020.03.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/04/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022]
Abstract
During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone-marrow-derived hematopoietic progenitors that migrate through the bloodstream. The current understanding of the nature of thymic immigrants is largely based on data from pre-clinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to examine the immature postnatal thymocyte population in humans. Integration of bone marrow and peripheral blood precursor datasets identified two putative thymus seeding progenitors that varied in expression of CD7; CD10; and the homing receptors CCR7, CCR9, and ITGB7. Whereas both precursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics underlying early human T lineage development, enabling prediction of transcription factor (TF) modules that drive stage-specific steps of human T cell development. This comprehensive dataset defines the expression signature of immature human thymocytes and provides a resource for the further study of human thymopoiesis.
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Affiliation(s)
- Marieke Lavaert
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium
| | - Kai Ling Liang
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Juliette Roels
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Monica S Kowalczyk
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Haematology Department, Royal Victoria Infirmary, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Bart Vandekerckhove
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Georges Leclercq
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Martin Guilliams
- Laboratory of Myeloid Cell Ontogeny and Functional Specialization, VIB Center for Inflammation Research, Ghent, Belgium; Faculty of Sciences, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Tom Taghon
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
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13
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Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses. Immunity 2020; 51:696-708.e9. [PMID: 31618654 DOI: 10.1016/j.immuni.2019.09.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/06/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022]
Abstract
Signaling abnormalities in immune responses in the small intestine can trigger chronic type 2 inflammation involving interaction of multiple immune cell types. To systematically characterize this response, we analyzed 58,067 immune cells from the mouse small intestine by single-cell RNA sequencing (scRNA-seq) at steady state and after induction of a type 2 inflammatory reaction to ovalbumin (OVA). Computational analysis revealed broad shifts in both cell-type composition and cell programs in response to the inflammation, especially in group 2 innate lymphoid cells (ILC2s). Inflammation induced the expression of exon 5 of Calca, which encodes the alpha-calcitonin gene-related peptide (α-CGRP), in intestinal KLRG1+ ILC2s. α-CGRP antagonized KLRG1+ ILC2s proliferation but promoted IL-5 expression. Genetic perturbation of α-CGRP increased the proportion of intestinal KLRG1+ ILC2s. Our work highlights a model where α-CGRP-mediated neuronal signaling is critical for suppressing ILC2 expansion and maintaining homeostasis of the type 2 immune machinery.
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Affiliation(s)
- Heping Xu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China; Laboratory of Systems Immunology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China.
| | - Jiarui Ding
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Antonia Wallrapp
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02114, USA
| | - Marcin Tabaka
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sai Ma
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shujie Fu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China; Laboratory of Systems Immunology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Xuanxuan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China; Laboratory of Systems Immunology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | | | - Chienwen Su
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Danielle Dionne
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lan T Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ariel Lefkovith
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrick R Burkett
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02114, USA
| | - Hai Ning Shi
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | | | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02114, USA
| | - Vijay K Kuchroo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02114, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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14
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Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M. Decoding human fetal liver haematopoiesis. Nature 2019; 574:365-371. [PMID: 31597962 PMCID: PMC6861135 DOI: 10.1038/s41586-019-1652-y] [Citation(s) in RCA: 310] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 09/09/2019] [Indexed: 11/09/2022]
Abstract
Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells and multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. Here, using single-cell transcriptome profiling of approximately 140,000 liver and 74,000 skin, kidney and yolk sac cells, we identify the repertoire of human blood and immune cells during development. We infer differentiation trajectories from HSC/MPPs and evaluate the influence of the tissue microenvironment on blood and immune cell development. We reveal physiological erythropoiesis in fetal skin and the presence of mast cells, natural killer and innate lymphoid cell precursors in the yolk sac. We demonstrate a shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs.
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Affiliation(s)
- Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Kile Green
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Simone Webb
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Emily F Calderbank
- Department of Haematology and Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Issac Goh
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Meghan Acres
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Maunder
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Peter Vegh
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Yorick Gitton
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhichao Miao
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - David Dixon
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel Rowell
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - David McDonald
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - James Fletcher
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Elizabeth Poyner
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gary Reynolds
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Michael Mather
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Corina Moldovan
- Department of Pathology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frankie Greig
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Steven Lisgo
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Fuller
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ben Millar
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Barbara Innes
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Monika S Kowalczyk
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Haematology Department, Royal Victoria Infirmary, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Peter Carey
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anindita Roy
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Irene Roberts
- Department of Paediatrics, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit and Department of Paediatrics, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Berthold Göttgens
- Department of Haematology and Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | - Elisa Laurenti
- Department of Haematology and Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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15
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Baryawno N, Przybylski D, Kowalczyk MS, Kfoury Y, Severe N, Gustafsson K, Kokkaliaris KD, Mercier F, Tabaka M, Hofree M, Dionne D, Papazian A, Lee D, Ashenberg O, Subramanian A, Vaishnav ED, Rozenblatt-Rosen O, Regev A, Scadden DT. A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia. Cell 2019; 177:1915-1932.e16. [PMID: 31130381 DOI: 10.1016/j.cell.2019.04.040] [Citation(s) in RCA: 512] [Impact Index Per Article: 102.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/05/2019] [Accepted: 04/23/2019] [Indexed: 01/23/2023]
Abstract
Stroma is a poorly defined non-parenchymal component of virtually every organ with key roles in organ development, homeostasis, and repair. Studies of the bone marrow stroma have defined individual populations in the stem cell niche regulating hematopoietic regeneration and capable of initiating leukemia. Here, we use single-cell RNA sequencing (scRNA-seq) to define a cellular taxonomy of the mouse bone marrow stroma and its perturbation by malignancy. We identified seventeen stromal subsets expressing distinct hematopoietic regulatory genes spanning new fibroblastic and osteoblastic subpopulations including distinct osteoblast differentiation trajectories. Emerging acute myeloid leukemia impaired mesenchymal osteogenic differentiation and reduced regulatory molecules necessary for normal hematopoiesis. These data suggest that tissue stroma responds to malignant cells by disadvantaging normal parenchymal cells. Our taxonomy of the stromal compartment provides a comprehensive bone marrow cell census and experimental support for cancer cell crosstalk with specific stromal elements to impair normal tissue function and thereby enable emergent cancer.
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Affiliation(s)
- Ninib Baryawno
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Childhood Cancer Research Unit, Dep. of Children's and Women's Health, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Dariusz Przybylski
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Monika S Kowalczyk
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Youmna Kfoury
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nicolas Severe
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Karin Gustafsson
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Konstantinos D Kokkaliaris
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Francois Mercier
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ani Papazian
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dongjun Lee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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16
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Schiebinger G, Shu J, Tabaka M, Cleary B, Subramanian V, Solomon A, Gould J, Liu S, Lin S, Berube P, Lee L, Chen J, Brumbaugh J, Rigollet P, Hochedlinger K, Jaenisch R, Regev A, Lander ES. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Cell 2019; 176:1517. [PMID: 30849376 DOI: 10.1016/j.cell.2019.02.026] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Schiebinger G, Shu J, Tabaka M, Cleary B, Subramanian V, Solomon A, Gould J, Liu S, Lin S, Berube P, Lee L, Chen J, Brumbaugh J, Rigollet P, Hochedlinger K, Jaenisch R, Regev A, Lander ES. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Cell 2019; 176:928-943.e22. [PMID: 30712874 PMCID: PMC6402800 DOI: 10.1016/j.cell.2019.01.006] [Citation(s) in RCA: 254] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/15/2018] [Accepted: 01/02/2019] [Indexed: 12/18/2022]
Abstract
Understanding the molecular programs that guide differentiation during development is a major challenge. Here, we introduce Waddington-OT, an approach for studying developmental time courses to infer ancestor-descendant fates and model the regulatory programs that underlie them. We apply the method to reconstruct the landscape of reprogramming from 315,000 single-cell RNA sequencing (scRNA-seq) profiles, collected at half-day intervals across 18 days. The results reveal a wider range of developmental programs than previously characterized. Cells gradually adopt either a terminal stromal state or a mesenchymal-to-epithelial transition state. The latter gives rise to populations related to pluripotent, extra-embryonic, and neural cells, with each harboring multiple finer subpopulations. The analysis predicts transcription factors and paracrine signals that affect fates and experiments validate that the TF Obox6 and the cytokine GDF9 enhance reprogramming efficiency. Our approach sheds light on the process and outcome of reprogramming and provides a framework applicable to diverse temporal processes in biology.
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Affiliation(s)
- Geoffrey Schiebinger
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; MIT Center for Statistics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jian Shu
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brian Cleary
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computational and Systems Biology Program, MIT, Cambridge, MA 02142, USA
| | - Vidya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aryeh Solomon
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Siyan Liu
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Biochemistry Program, Wellesley College, Wellesley, MA 02481, USA
| | - Stacie Lin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter Berube
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lia Lee
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jenny Chen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Justin Brumbaugh
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Philippe Rigollet
- MIT Center for Statistics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Computational and Systems Biology Program, MIT, Cambridge, MA 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Eric S Lander
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Systems Biology Harvard Medical School, Boston, MA 02125, USA.
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18
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Ochab-Marcinek A, Jędrak J, Tabaka M. Hill kinetics as a noise filter: the role of transcription factor autoregulation in gene cascades. Phys Chem Chem Phys 2018; 19:22580-22591. [PMID: 28809965 DOI: 10.1039/c7cp00743d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An intuition based on deterministic models of chemical kinetics is that population heterogeneity of transcription factor levels in cells is transmitted unchanged downstream to the target genes. We use a stochastic model of a two-gene cascade with a self-regulating upstream gene to show that, counter to the intuition, there is no simple mapping (bimodal to bimodal, unimodal to unimodal) between the shapes of the distributions of transcription factor numbers and target protein numbers in cells. Due to the presence of the two regulations, the system contains two nonlinear transfer functions, defined by the Hill kinetics of transcription factor binding. The transfer function of the regulator can "interfere" with the transfer function of the target, converting the bimodal input into a unimodal output or vice versa. We show that this effect can be predicted by a geometric construction. As an example application of the method, we present a case study of a system of several downstream genes of different sensitivities, controlled by a common transcription factor which also regulates its own transcription. We show that a single regulator can induce qualitatively different patterns (binary or graded) of responses to a signal in different downstream genes, depending on whether the sensitivity regions of the transfer functions of the upstream and downstream genes overlap or not. Alternatively, the same model can be interpreted as describing a single downstream gene that has different sensitivities in different cell lines due to mutations. Our model shows, therefore, a possible kinetic mechanism by which different genes can interpret the same biological signal in a different manner.
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Affiliation(s)
- Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Jakub Jędrak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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19
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Shen Z, Kang J, Shakya A, Tabaka M, Jarboe EA, Regev A, Tantin D. Enforcement of developmental lineage specificity by transcription factor Oct1. eLife 2017; 6:20937. [PMID: 28537559 PMCID: PMC5466424 DOI: 10.7554/elife.20937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/23/2017] [Indexed: 12/26/2022] Open
Abstract
Embryonic stem cells co-express Oct4 and Oct1, a related protein with similar DNA-binding specificity. To study the role of Oct1 in ESC pluripotency and transcriptional control, we constructed germline and inducible-conditional Oct1-deficient ESC lines. ESCs lacking Oct1 show normal appearance, self-renewal and growth but manifest defects upon differentiation. They fail to form beating cardiomyocytes, generate neurons poorly, form small, poorly differentiated teratomas, and cannot generate chimeric mice. Upon RA-mediated differentiation, Oct1-deficient cells induce lineage-appropriate developmentally poised genes poorly while lineage-inappropriate genes, including extra-embryonic genes, are aberrantly expressed. In ESCs, Oct1 co-occupies a specific set of targets with Oct4, but does not occupy differentially expressed developmental targets. Instead, Oct1 occupies these targets as cells differentiate and Oct4 declines. These results identify a dynamic interplay between Oct1 and Oct4, in particular during the critical window immediately after loss of pluripotency when cells make the earliest developmental fate decisions. DOI:http://dx.doi.org/10.7554/eLife.20937.001 Humans and most other animals are composed of hundreds of different types of cell, including nerve cells, muscle cells and blood cells. Despite performing many different roles, these cells all develop from a single fertilized egg, which divides to make a particular group of cells that when studied in the laboratory are called embryonic stem cells (or ESCs for short). The ability of a cell to become a different cell type is defined as “potency”. ESCs are unique because they can specialize into any type of cell present in the adult organism, and they are therefore called “pluripotent”. However, as the embryo develops, its ESCs gradually lose their potency, and become more and more specialized. The activity of a great number of genes must be regulated during the transition from pluripotent to specialized cells, and some of the mechanisms involved in this transition are still unclear. ESCs are known to need a gene-regulating protein called Oct4 to remain pluripotent and Shen, Kang, Shakya et al. now show that a similar protein named Oct1 is essential for their transition to becoming more specialized. When the gene for Oct1 was deleted from mouse ECSs, they behaved largely like “normal” ESCs, but could not properly mature into certain cell types such as heart and nerve cells. Molecular analyses revealed that Oct4 and Oct1 compete to regulate the activity of many common genes with opposing outcomes: Oct4 keeps ESCs pluripotent while Oct1 leads them to specialize. The Oct4 protein is abundant in ESCs and prevails over Oct1, but as the cells mature, the levels of Oct4 drop, and Oct1 takes over in the regulation of their common target genes. Going forward, a better understanding of how ESCs become specialized will help basic research in the laboratory and allow scientists to tackle new questions about how the human body develops and how our organs work. In the longer-term, these findings might also have applications in the field of regenerative medicine, which aims to repair or replace a person’s cells, tissues or organs to improve their health. DOI:http://dx.doi.org/10.7554/eLife.20937.002
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Affiliation(s)
- Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Jinsuk Kang
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Arvind Shakya
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Marcin Tabaka
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Elke A Jarboe
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
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Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. PLoS One 2016; 11:e0152002. [PMID: 27008630 PMCID: PMC4805274 DOI: 10.1371/journal.pone.0152002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/06/2016] [Indexed: 11/30/2022] Open
Abstract
LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.
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Affiliation(s)
- Lili Sun
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, 29634, United States of America
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Seattle, Washington, 98195–4350, United States of America
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Christopher Maffeo
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Xuzhu Zhang
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
- * E-mail:
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Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. PLoS One 2016; 11:e0152002. [PMID: 27008630 DOI: 10.1371/joumal.pone.0152002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/06/2016] [Indexed: 05/27/2023] Open
Abstract
LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.
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Affiliation(s)
- Lili Sun
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, 29634, United States of America
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Seattle, Washington, 98195-4350, United States of America
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Christopher Maffeo
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Xuzhu Zhang
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
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Sozański K, Ruhnow F, Wiśniewska A, Tabaka M, Diez S, Hołyst R. Small Crowders Slow Down Kinesin-1 Stepping by Hindering Motor Domain Diffusion. Phys Rev Lett 2015; 115:218102. [PMID: 26636875 DOI: 10.1103/physrevlett.115.218102] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Indexed: 05/23/2023]
Abstract
The dimeric motor protein kinesin-1 moves processively along microtubules against forces of up to 7 pN. However, the mechanism of force generation is still debated. Here, we point to the crucial importance of diffusion of the tethered motor domain for the stepping of kinesin-1: small crowders stop the motor at a viscosity of 5 mPa·s-corresponding to a hydrodynamic load in the sub-fN (~10^{-4} pN) range-whereas large crowders have no impact even at viscosities above 100 mPa·s. This indicates that the scale-dependent, effective viscosity experienced by the tethered motor domain is a key factor determining kinesin's functionality. Our results emphasize the role of diffusion in the kinesin-1 stepping mechanism and the general importance of the viscosity scaling paradigm in nanomechanics.
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Affiliation(s)
- Krzysztof Sozański
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Felix Ruhnow
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstrasse 18, 01307 Dresden, Germany
| | - Agnieszka Wiśniewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Stefan Diez
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstrasse 18, 01307 Dresden, Germany
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Kalwarczyk T, Sozanski K, Ochab-Marcinek A, Szymanski J, Tabaka M, Hou S, Holyst R. Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model. Adv Colloid Interface Sci 2015; 223:55-63. [PMID: 26189602 DOI: 10.1016/j.cis.2015.06.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/27/2015] [Accepted: 06/27/2015] [Indexed: 01/12/2023]
Abstract
This paper deals with the recent phenomenological model of the motion of nanoscopic objects (colloidal particles, proteins, nanoparticles, molecules) in complex liquids. We analysed motion in polymer, micellar, colloidal and protein solutions and the cytoplasm of living cells using the length-scale dependent viscosity model. Viscosity monotonically approaches macroscopic viscosity as the size of the object increases and thus gives a single, coherent picture of motion at the nano and macro scale. The model includes interparticle interactions (solvent-solute), temperature and the internal structure of a complex liquid. The depletion layer ubiquitously occurring in complex liquids is also incorporated into the model. We also discuss the biological aspects of crowding in terms of the length-scale dependent viscosity model.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Sozanski
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Anna Ochab-Marcinek
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Jedrzej Szymanski
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; State Key Laboratory of Medicinal Chemical Biology, Nankai University, China
| | - Robert Holyst
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Tabaka M, Burdzy K, Hołyst R. Method for the analysis of contribution of sliding and hopping to a facilitated diffusion of DNA-binding protein: Application to in vivo data. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 92:022721. [PMID: 26382446 DOI: 10.1103/physreve.92.022721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 06/05/2023]
Abstract
DNA-binding protein searches for its target, a specific site on DNA, by means of diffusion. The search process consists of many recurrent steps of one-dimensional diffusion (sliding) along the DNA chain and three-dimensional diffusion (hopping) after dissociation of a protein from the DNA chain. Here we propose a computational method that allows extracting the contribution of sliding and hopping to the search process in vivo from the measurements of the kinetics of the target search by the lac repressor in Escherichia coli [P. Hammar et al., Science 336, 1595 (2012)]. The method combines lattice Monte Carlo simulations with the Brownian excursion theory and includes explicitly steric constraints for hopping due to the helical structure of DNA. The simulation results including all experimental data reveal that the in vivo target search is dominated by sliding. The short-range hopping to the same base pair interrupts one-dimensional sliding while long-range hopping does not contribute significantly to the kinetics of the search of the target in vivo.
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Affiliation(s)
- Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Box 354350, Seattle, Washington 98195, USA
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Ochab-Marcinek A, Tabaka M. Transcriptional leakage versus noise: a simple mechanism of conversion between binary and graded response in autoregulated genes. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:012704. [PMID: 25679640 DOI: 10.1103/physreve.91.012704] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 06/04/2023]
Abstract
We study the response of an autoregulated gene to a range of concentrations of signal molecules. We show that transcriptional leakage and noise due to translational bursting have the opposite effects. In a positively autoregulated gene, increasing the noise converts the response from graded to binary, while increasing the leakage converts the response from binary to graded. Our findings support the hypothesis that, being a common phenomenon, leaky expression may be a relatively easy way for evolutionary tuning of the type of gene response without changing the type of regulation from positive to negative.
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Affiliation(s)
- Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
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26
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Abstract
We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between for large proteins up to for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1–2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance.
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Affiliation(s)
- Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka, 01-224 Warsaw, Poland
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Lewandrowska A, Majcher A, Ochab-Marcinek A, Tabaka M, Hołyst R. Taylor Dispersion Analysis in Coiled Capillaries at High Flow Rates. Anal Chem 2013; 85:4051-6. [DOI: 10.1021/ac4007792] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Lewandrowska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Poland
| | - Aldona Majcher
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Poland
| | - Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Poland
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Poland
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Abstract
Motivation: Biologistics provides data for quantitative analysis of transport (diffusion) processes and their spatio-temporal correlations in cells. Mobility of proteins is one of the few parameters necessary to describe reaction rates for gene regulation. Although understanding of diffusion-limited biochemical reactions in vivo requires mobility data for the largest possible number of proteins in their native forms, currently, there is no database that would contain the complete information about the diffusion coefficients (DCs) of proteins in a given cell type. Results: We demonstrate a method for the determination of in vivo DCs for any molecule—regardless of its molecular weight, size and structure—in any type of cell. We exemplify the method with the database of in vivo DC for all proteins (4302 records) from the proteome of K12 strain of Escherichia coli, together with examples of DC of amino acids, sugars, RNA and DNA. The database follows from the scale-dependent viscosity reference curve (sdVRC). Construction of sdVRC for prokaryotic or eukaryotic cell requires ~20 in vivo measurements using techniques such as fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), nuclear magnetic resonance (NMR) or particle tracking. The shape of the sdVRC would be different for each organism, but the mathematical form of the curve remains the same. The presented method has a high predictive power, as the measurements of DCs of several inert, properly chosen probes in a single cell type allows to determine the DCs of thousands of proteins. Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo. Contact:rholyst@ichf.edu.pl Supplementary information:Supplementary data are available at Bioinformatics Online.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Hou S, Wieczorek SA, Kaminski TS, Ziebacz N, Tabaka M, Sorto NA, Foss MH, Shaw JT, Thanbichler M, Weibel DB, Nieznanski K, Holyst R, Garstecki P. Characterization of Caulobacter crescentus FtsZ protein using dynamic light scattering. J Biol Chem 2012; 287:23878-86. [PMID: 22573335 DOI: 10.1074/jbc.m111.309492] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The self-assembly of the tubulin homologue FtsZ at the mid-cell is a critical step in bacterial cell division. We introduce dynamic light scattering (DLS) spectroscopy as a new method to study the polymerization kinetics of FtsZ in solution. Analysis of the DLS data indicates that the FtsZ polymers are remarkably monodisperse in length, independent of the concentrations of GTP, GDP, and FtsZ monomers. Measurements of the diffusion coefficient of the polymers demonstrate that their length is remarkably stable until the free GTP is consumed. We estimated the mean size of the FtsZ polymers within this interval of stable length to be between 9 and 18 monomers. The rates of FtsZ polymerization and depolymerization are likely influenced by the concentration of GDP, as the repeated addition of GTP to FtsZ increased the rate of polymerization and slowed down depolymerization. Increasing the FtsZ concentration did not change the size of FtsZ polymers; however, it increased the rate of the depolymerization reaction by depleting free GTP. Using transmission electron microscopy we observed that FtsZ forms linear polymers in solutions which rapidly convert to large bundles upon contact with surfaces at time scales as short as several seconds. Finally, the best studied small molecule that binds to FtsZ, PC190723, had no stabilizing effect on Caulobacter crescentus FtsZ filaments in vitro, which complements previous studies with Escherichia coli FtsZ and confirms that this class of small molecules binds Gram-negative FtsZ weakly.
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Affiliation(s)
- Sen Hou
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Tabaka M, Hołyst R. Binary and graded evolution in time in a simple model of gene induction. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 82:052902. [PMID: 21230531 DOI: 10.1103/physreve.82.052902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Indexed: 05/30/2023]
Abstract
We solve analytically the model of gene expression induction which consists of three steps: gene activation, gene products synthesis, and product degradation. The solution is given as a time-dependent probability distribution for gene products. Following the distribution in time from the inactive state of the gene to the stationary state we observe binary or graded response depending solely on the ratio r of the gene activation rate to the rate of the gene product degradation. If r << 1 the response is binary and the continuous transition from binary to graded response occurs between r=0.1 and r=1. Therefore, if binary response is observed during relaxation to steady state, then the activation rate constant must be smaller than the degradation rate constant.
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Affiliation(s)
- Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Holyst R, Bielejewska A, Szymański J, Wilk A, Patkowski A, Gapiński J, Żywociński A, Kalwarczyk T, Kalwarczyk E, Tabaka M, Ziębacz N, Wieczorek SA. Scaling form of viscosity at all length-scales in poly(ethylene glycol) solutions studied by fluorescence correlation spectroscopy and capillary electrophoresis. Phys Chem Chem Phys 2009; 11:9025-32. [DOI: 10.1039/b908386c] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tabaka M, Cybulski O, Hołyst R. Accurate Genetic Switch in Escherichia coli: Novel Mechanism of Regulation by Co-repressor. J Mol Biol 2008; 377:1002-14. [DOI: 10.1016/j.jmb.2008.01.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2007] [Revised: 12/27/2007] [Accepted: 01/15/2008] [Indexed: 11/24/2022]
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