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Ramaswami G, Yuva-Aydemir Y, Akerberg B, Matthews B, Williams J, Golczer G, Huang J, Al Abdullatif A, Huh D, Burkly LC, Engle SJ, Grossman I, Sehgal A, Sigova AA, Fremeau RT, Liu Y, Bumcrot D. Author Correction: Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration. Sci Rep 2024; 14:9346. [PMID: 38654092 DOI: 10.1038/s41598-024-60234-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Affiliation(s)
| | | | | | | | | | | | - Jiaqi Huang
- CAMP4 Therapeutics Corporation, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | - Yuting Liu
- CAMP4 Therapeutics Corporation, Cambridge, MA, USA
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2
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Ramaswami G, Yuva-Aydemir Y, Akerberg B, Matthews B, Williams J, Golczer G, Huang J, Al Abdullatif A, Huh D, Burkly LC, Engle SJ, Grossman I, Sehgal A, Sigova AA, Fremeau RT, Liu Y, Bumcrot D. Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration. Sci Rep 2024; 14:2153. [PMID: 38272949 PMCID: PMC10810793 DOI: 10.1038/s41598-024-52311-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Microglia are the resident immune cells in the brain that play a key role in driving neuroinflammation, a hallmark of neurodegenerative disorders. Inducible microglia-like cells have been developed as an in vitro platform for molecular and therapeutic hypothesis generation and testing. However, there has been no systematic assessment of similarity of these cells to primary human microglia along with their responsiveness to external cues expected of primary cells in the brain. In this study, we performed transcriptional characterization of commercially available human inducible pluripotent stem cell (iPSC)-derived microglia-like (iMGL) cells by bulk and single cell RNA sequencing to assess their similarity with primary human microglia. To evaluate their stimulation responsiveness, iMGL cells were treated with Liver X Receptor (LXR) pathway agonists and their transcriptional responses characterized by bulk and single cell RNA sequencing. Bulk transcriptome analyses demonstrate that iMGL cells have a similar overall expression profile to freshly isolated human primary microglia and express many key microglial transcription factors and functional and disease-associated genes. Notably, at the single-cell level, iMGL cells exhibit distinct transcriptional subpopulations, representing both homeostatic and activated states present in normal and diseased primary microglia. Treatment of iMGL cells with LXR pathway agonists induces robust transcriptional changes in lipid metabolism and cell cycle at the bulk level. At the single cell level, we observe heterogeneity in responses between cell subpopulations in homeostatic and activated states and deconvolute bulk expression changes into their corresponding single cell states. In summary, our results demonstrate that iMGL cells exhibit a complex transcriptional profile and responsiveness, reminiscent of in vivo microglia, and thus represent a promising model system for therapeutic development in neurodegeneration.
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Affiliation(s)
| | | | | | | | | | | | - Jiaqi Huang
- CAMP4 Therapeutics Corporation, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | - Yuting Liu
- CAMP4 Therapeutics Corporation, Cambridge, MA, USA
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3
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Li K, Sun YH, Ouyang Z, Negi S, Gao Z, Zhu J, Wang W, Chen Y, Piya S, Hu W, Zavodszky MI, Yalamanchili H, Cao S, Gehrke A, Sheehan M, Huh D, Casey F, Zhang X, Zhang B. scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing. BMC Genomics 2023; 24:228. [PMID: 37131143 PMCID: PMC10155351 DOI: 10.1186/s12864-023-09332-2] [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: 01/17/2023] [Accepted: 04/25/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing is a state-of-the-art technology to understand gene expression in complex tissues. With the growing amount of data being generated, the standardization and automation of data analysis are critical to generating hypotheses and discovering biological insights. RESULTS Here, we present scRNASequest, a semi-automated single-cell RNA-seq (scRNA-seq) data analysis workflow which allows (1) preprocessing from raw UMI count data, (2) harmonization by one or multiple methods, (3) reference-dataset-based cell type label transfer and embedding projection, (4) multi-sample, multi-condition single-cell level differential gene expression analysis, and (5) seamless integration with cellxgene VIP for visualization and with CellDepot for data hosting and sharing by generating compatible h5ad files. CONCLUSIONS We developed scRNASequest, an end-to-end pipeline for single-cell RNA-seq data analysis, visualization, and publishing. The source code under MIT open-source license is provided at https://github.com/interactivereport/scRNASequest . We also prepared a bookdown tutorial for the installation and detailed usage of the pipeline: https://interactivereport.github.io/scRNAsequest/tutorial/docs/ . Users have the option to run it on a local computer with a Linux/Unix system including MacOS, or interact with SGE/Slurm schedulers on high-performance computing (HPC) clusters.
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Affiliation(s)
- Kejie Li
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Yu H Sun
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | | | - Soumya Negi
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Zhen Gao
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Jing Zhu
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Wanli Wang
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Yirui Chen
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Sarbottam Piya
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Wenxing Hu
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Maria I Zavodszky
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Hima Yalamanchili
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Shaolong Cao
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Andrew Gehrke
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Mark Sheehan
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Dann Huh
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Fergal Casey
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA
| | - Xinmin Zhang
- Data Science, BioInfoRx Inc., Madison, WI, 53719, USA
| | - Baohong Zhang
- Research Data Sciences, Translational Biology, Biogen Inc., Cambridge, MA, 02142, USA.
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4
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Delbridge ARD, Huh D, Brickelmaier M, Burns JC, Roberts C, Challa R, Raymond N, Cullen P, Carlile TM, Ennis KA, Liu M, Sun C, Allaire NE, Foos M, Tsai HH, Franchimont N, Ransohoff RM, Butts C, Mingueneau M. Organotypic Brain Slice Culture Microglia Exhibit Molecular Similarity to Acutely-Isolated Adult Microglia and Provide a Platform to Study Neuroinflammation. Front Cell Neurosci 2020; 14:592005. [PMID: 33473245 PMCID: PMC7812919 DOI: 10.3389/fncel.2020.592005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 08/06/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Microglia are central nervous system (CNS) resident immune cells that have been implicated in neuroinflammatory pathogenesis of a variety of neurological conditions. Their manifold context-dependent contributions to neuroinflammation are only beginning to be elucidated, which can be attributed in part to the challenges of studying microglia in vivo and the lack of tractable in vitro systems to study microglia function. Organotypic brain slice cultures offer a tissue-relevant context that enables the study of CNS resident cells and the analysis of brain slice microglial phenotypes has provided important insights, in particular into neuroprotective functions. Here we use RNA sequencing, direct digital quantification of gene expression with nCounter® technology and targeted analysis of individual microglial signature genes, to characterize brain slice microglia relative to acutely-isolated counterparts and 2-dimensional (2D) primary microglia cultures, a widely used in vitro surrogate. Analysis using single cell and population-based methods found brain slice microglia exhibited better preservation of canonical microglia markers and overall gene expression with stronger fidelity to acutely-isolated adult microglia, relative to in vitro cells. We characterized the dynamic phenotypic changes of brain slice microglia over time, after plating in culture. Mechanical damage associated with slice preparation prompted an initial period of inflammation, which resolved over time. Based on flow cytometry and gene expression profiling we identified the 2-week timepoint as optimal for investigation of microglia responses to exogenously-applied stimuli as exemplified by treatment-induced neuroinflammatory changes observed in microglia following LPS, TNF and GM-CSF addition to the culture medium. Altogether these findings indicate that brain slice cultures provide an experimental system superior to in vitro culture of microglia as a surrogate to investigate microglia functions, and the impact of soluble factors and cellular context on their physiology.
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Affiliation(s)
- Alex R D Delbridge
- Multiple Sclerosis and Neuroimmunology Research Unit, Biogen, Cambridge, MA, United States.,Biogen Postdoctoral Scientist Program, Biogen, Cambridge, MA, United States
| | - Dann Huh
- Translational Biology, Biogen, Cambridge, MA, United States
| | - Margot Brickelmaier
- Multiple Sclerosis and Neuroimmunology Research Unit, Biogen, Cambridge, MA, United States
| | - Jeremy C Burns
- Multiple Sclerosis and Neuroimmunology Research Unit, Biogen, Cambridge, MA, United States
| | - Chris Roberts
- Translational Biology, Biogen, Cambridge, MA, United States
| | - Ravi Challa
- Translational Biology, Biogen, Cambridge, MA, United States
| | - Naideline Raymond
- Multiple Sclerosis and Neuroimmunology Research Unit, Biogen, Cambridge, MA, United States
| | - Patrick Cullen
- Translational Biology, Biogen, Cambridge, MA, United States
| | | | - Katelin A Ennis
- Genetic and Neurodevelopmental Disorders, Biogen, Cambridge, MA, United States
| | - Mei Liu
- Biogen Postdoctoral Scientist Program, Biogen, Cambridge, MA, United States
| | - Chao Sun
- Biogen Postdoctoral Scientist Program, Biogen, Cambridge, MA, United States
| | - Normand E Allaire
- Biogen Postdoctoral Scientist Program, Biogen, Cambridge, MA, United States
| | - Marianna Foos
- Biogen Postdoctoral Scientist Program, Biogen, Cambridge, MA, United States
| | - Hui-Hsin Tsai
- Multiple Sclerosis and Neuroimmunology Research Unit, Biogen, Cambridge, MA, United States
| | | | - Richard M Ransohoff
- Multiple Sclerosis and Neuroimmunology Research Unit, Biogen, Cambridge, MA, United States
| | - Cherie Butts
- Digital & Quantitative Medicine, Biogen, Cambridge, MA, United States
| | - Michael Mingueneau
- Multiple Sclerosis and Neuroimmunology Research Unit, Biogen, Cambridge, MA, United States
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5
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Pearson CR, Kaysen D, Huh D, Bedard-Gillgan M, Walker D, Marin R, Saluskin K. A randomized comparison trial of culturally adapted HIV prevention approaches for Native Americans reducing trauma symptoms versus substance misuse: The Healing Seasons protocol. Contemp Clin Trials 2020; 95:106070. [PMID: 32561467 DOI: 10.1016/j.cct.2020.106070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/27/2020] [Accepted: 06/12/2020] [Indexed: 11/28/2022]
Abstract
Native Americans (NA) experience interrelated risks of trauma exposure, substance use, and HIV risk behaviors that put them at increased risk for HIV infection. Despite these known risk factors, there are very few published randomized trials testing interventions to reduce trauma-related symptoms and substance misuse among NA. METHODS The Healing Seasons study is a randomized comparsion trial of two counseling strategies, Narrative Exposure Therapy (NET) addressing PTSD or Motivational interviewing with cognitive behavioral therapy skills training (MIST) addressing substance misuse as a means to prevent HIV among NA. Using a community-based participatory research approach, we adapted both evidence-based interventions to be specific to the risk contexts and realities of NA and to include psychoeducational and skill-building components that include cultural-specific stories, virtues, and traditional treatment strategies. Participants, 16 years and older, were recruited from a Pacific Northwest tribal community, screened over the phone, enrolled in person, and randomized in equal numbers to NET or MIST. We stratified by age (16-29 years and 30 or older) and gender (male or female identified) to ensure balance between treatment arms. The primary outcomes were number of sex partners and frequency of sexual acts (with and without condoms), sex under the influence of substances, frequency of substance use, and PTSD severity. DISCUSSION Behavioral interventions for NA are needed to prevent HIV risk behaviors when faced with trauma symptoms and substance misuse. This study will provide evidence to determine feasibility and efficacy of addressing related risk factors as part of counseling-based HIV prevention intervention to reduce sexual risk among this population. TRIAL REGISTRATION ClinicalTrials.gov number, NCT03112369, registered April 12, 2017.
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Affiliation(s)
- C R Pearson
- Indigenous Wellness Research Institute, School of Social Work, University of Washington, Seattle, WA, USA.
| | - D Kaysen
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - D Huh
- Indigenous Wellness Research Institute, School of Social Work, University of Washington, Seattle, WA, USA
| | - M Bedard-Gillgan
- Department of Psychiatry, University of Washington, Seattle, WA, USA
| | - D Walker
- Innovative Programs Research Group, School of Social Work, University of Washington, Seattle, WA, USA
| | - R Marin
- Indigenous Wellness Research Institute, School of Social Work, University of Washington, Seattle, WA, USA
| | - K Saluskin
- Yakama Nation Behavioral Health Services, Toppenish, WA, USA
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6
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You J, Farrell M, Zheng Y, Yang R, Nace A, Huh D, Cotsarelis G. 925 Small molecule targeting of multiple signaling pathways for hair follicle formation from mouse neonatal cells. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.03.1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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7
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Ofengeim D, Giagtzoglou N, Huh D, Zou C, Yuan J. Single-Cell RNA Sequencing: Unraveling the Brain One Cell at a Time. Trends Mol Med 2017; 23:563-576. [PMID: 28501348 DOI: 10.1016/j.molmed.2017.04.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/13/2017] [Accepted: 04/13/2017] [Indexed: 12/16/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is an exciting new technology allowing the analysis of transcriptomes from individual cells, and is ideally suited to address the inherent complexity and dynamics of the central nervous system. scRNA-seq has already been applied to the study of molecular taxonomy of the brain. These works have paved the way to expanding our understanding of the nervous system and provide insights into cellular susceptibilities and molecular mechanisms in neurological and neurodegenerative diseases. We discuss recent progress and challenges in applying this technology to advance our understanding of the brain. We advocate the application of scRNA-seq in the discovery of targets and biomarkers as a new approach in developing novel therapeutics for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Dimitry Ofengeim
- Biogen, Neurology, 115 Broadway Street, Cambridge, MA 02142, USA.
| | | | - Dann Huh
- Biogen, Neurology, 115 Broadway Street, Cambridge, MA 02142, USA
| | - Chengyu Zou
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Junying Yuan
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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8
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Landgraf D, Huh D, Hallacli E, Lindquist S. Scarless Gene Tagging with One-Step Transformation and Two-Step Selection in Saccharomyces cerevisiae and Schizosaccharomyces pombe. PLoS One 2016; 11:e0163950. [PMID: 27736907 PMCID: PMC5063382 DOI: 10.1371/journal.pone.0163950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 09/16/2016] [Indexed: 11/24/2022] Open
Abstract
Gene tagging with fluorescent proteins is commonly applied to investigate the localization and dynamics of proteins in their cellular environment. Ideally, a fluorescent tag is genetically inserted at the endogenous locus at the N- or C- terminus of the gene of interest without disrupting regulatory sequences including the 5’ and 3’ untranslated region (UTR) and without introducing any extraneous unwanted “scar” sequences, which may create unpredictable transcriptional or translational effects. We present a reliable, low-cost, and highly efficient method for the construction of such scarless C-terminal and N-terminal fusions with fluorescent proteins in yeast. The method relies on sequential positive and negative selection and uses an integration cassette with long flanking regions, which is assembled by two-step PCR, to increase the homologous recombination frequency. The method also enables scarless tagging of essential genes with no need for a complementing plasmid. To further ease high-throughput strain construction, we have computationally automated design of the primers, applied the primer design code to all open reading frames (ORFs) of the budding yeast Saccharomyces cerevisiae (S. cerevisiae) and the fission yeast Schizosaccharomyces pombe (S. pombe), and provide here the computed sequences. To illustrate the scarless N- and C-terminal gene tagging methods in S. cerevisiae, we tagged various genes including the E3 ubiquitin ligase RSP5, the proteasome subunit PRE1, and the eleven Rab GTPases with yeast codon-optimized mNeonGreen or mCherry; several of these represent essential genes. We also implemented the scarless C-terminal gene tagging method in the distantly related organism S. pombe using kanMX6 and HSV1tk as positive and negative selection markers, respectively, as well as ura4. The scarless gene tagging methods presented here are widely applicable to visualize and investigate the functional roles of proteins in living cells.
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Affiliation(s)
- Dirk Landgraf
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Dann Huh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Erinc Hallacli
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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9
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Okumus B, Landgraf D, Lai GC, Bakshi S, Arias-Castro JC, Yildiz S, Huh D, Fernandez-Lopez R, Peterson CN, Toprak E, El Karoui M, Paulsson J. Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells. Nat Commun 2016; 7:11641. [PMID: 27189321 PMCID: PMC4873973 DOI: 10.1038/ncomms11641] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/15/2016] [Indexed: 11/18/2022] Open
Abstract
Many key regulatory proteins in bacteria are present in too low numbers to be detected with conventional methods, which poses a particular challenge for single-cell analyses because such proteins can contribute greatly to phenotypic heterogeneity. Here we develop a microfluidics-based platform that enables single-molecule counting of low-abundance proteins by mechanically slowing-down their diffusion within the cytoplasm of live Escherichia coli (E. coli) cells. Our technique also allows for automated microscopy at high throughput with minimal perturbation to native physiology, as well as viable enrichment/retrieval. We illustrate the method by analysing the control of the master regulator of the E. coli stress response, RpoS, by its adapter protein, SprE (RssB). Quantification of SprE numbers shows that though SprE is necessary for RpoS degradation, it is expressed at levels as low as 3–4 molecules per average cell cycle, and fluctuations in SprE are approximately Poisson distributed during exponential phase with no sign of bursting. Several proteins are expressed at too low abundance in the Escherichia coli (E. coli) proteome to be detected by standard methods. Here, the authors create a microfluidics-based platform enabling single-molecule counting of low-abundance proteins by mechanically slowing-down their diffusion in live E. coli.
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Affiliation(s)
- Burak Okumus
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dirk Landgraf
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ghee Chuan Lai
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Somenath Bakshi
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Juan Carlos Arias-Castro
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Physics, Universidad de los Andes, Bogota 4976-12340, Colombia
| | - Sadik Yildiz
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dann Huh
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Raul Fernandez-Lopez
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Celeste N Peterson
- Department of Biology, Suffolk University, Boston, Massachusetts 02108, USA
| | - Erdal Toprak
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Meriem El Karoui
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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10
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Abstract
All cellular materials are partitioned between daughters at cell division, but by various mechanisms and with different accuracy. In the yeast Schizosaccharomyces pombe, the mitochondria are pushed to the cell poles by the spindle. We found that mitochondria spatially reequilibrate just before division, and that the mitochondrial volume and DNA-containing nucleoids instead segregate in proportion to the cytoplasm inherited by each daughter. However, nucleoid partitioning errors are suppressed by control at two levels: Mitochondrial volume is actively distributed throughout a cell, and nucleoids are spaced out in semiregular arrays within mitochondria. During the cell cycle, both mitochondria and nucleoids appear to be produced without feedback, creating a net control of fluctuations that is just accurate enough to avoid substantial growth defects.
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Affiliation(s)
- Rishi Jajoo
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yoonseok Jung
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dann Huh
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Matheus P Viana
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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11
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Okumus B, Fernandez-Lopez R, Landgraf D, Huh D, Paulsson J. Microfluidics Assisted Cell Screening. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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12
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Abstract
Many RNAs, proteins, and organelles are present in such low numbers per cell that random segregation of individual copies causes large "partitioning errors" at cell division. Even symmetrically dividing cells can then by chance produce daughters with very different composition. The size of the errors depends on the segregation mechanism: Control systems can reduce low-abundance errors, but the segregation process can also be subject to upstream sources of randomness or spatial heterogeneities that create large errors despite high abundances. Here we mathematically demonstrate how partitioning errors arise for different types of segregation mechanisms and how errors can be greatly increased by upstream heterogeneity but remarkably hard to avoid through controlled partitioning. We also show that seemingly straightforward experiments cannot be straightforwardly interpreted because very different mechanisms produce identical fits and present an approach to deal with this problem by adding binomial counting noise and testing for convexity or concavity in the partitioning error as a function of the binomial thinning parameter. The results lay a conceptual groundwork for more effective studies of heterogeneity among growing and dividing cells, whether in microbes or in differentiating tissues.
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Affiliation(s)
- Dann Huh
- Department of Systems Biology, Harvard University, Boston, MA 02115; and
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Johan Paulsson
- Department of Systems Biology, Harvard University, Boston, MA 02115; and
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13
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Abstract
Gene expression involves inherently probabilistic steps that create fluctuations in protein abundances. The results from many in-depth analyses and genome-scale surveys have suggested how such fluctuations arise and spread, often in ways consistent with stochastic models of transcription and translation. But fluctuations also arise during cell division when molecules are partitioned stochastically between the two daughters. Here we mathematically demonstrate how stochastic partitioning contributes to the non-genetic heterogeneity. Our results show that partitioning errors are hard to correct, and that the resulting noise profiles are remarkably difficult to separate from gene expression noise. By applying these results to common experimental strategies and distinguishing between creation versus transmission of noise, we hypothesize that much of the cell-to-cell heterogeneity that has been attributed to various aspects of gene expression instead comes from random segregation at cell division. We propose experiments to separate between these two types of fluctuations and discuss future directions.
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Affiliation(s)
- Dann Huh
- Department of Systems Biology, Harvard University, Boston, Massachusetts, USA
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14
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Zheng Y, Fujioka H, Bian S, Torisawa Y, Huh D, Takayama S, Grotberg JB. Liquid plug propagation in flexible microchannels: A small airway model. Phys Fluids (1994) 2009; 21:71903. [PMID: 19704915 PMCID: PMC2730709 DOI: 10.1063/1.3183777] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 06/23/2009] [Indexed: 05/02/2023]
Abstract
In the present study, we investigate the effect of wall flexibility on the plug propagation and the resulting wall stresses in small airway models with experimental measurements and numerical simulations. Experimentally, a flexible microchannel was fabricated to mimic the flexible small airways using soft lithography. Liquid plugs were generated and propagated through the microchannels. The local wall deformation is observed instantaneously during plug propagation with the maximum increasing with plug speed. The pressure drop across the plug is measured and observed to increase with plug speed, and is slightly smaller in a flexible channel compared to that in a rigid channel. A computational model is then presented to model the steady plug propagation through a flexible channel corresponding to the middle plane in the experimental device. The results show qualitative agreements with experiments on wall shapes and pressure drops and the discrepancies bring up interesting questions on current field of modeling. The flexible wall deforms inward near the plug core region, the deformation and pressure drop across the plug increase with the plug speed. The wall deformation and resulting stresses vary with different longitudinal tensions, i.e., for large wall longitudinal tension, the wall deforms slightly, which causes decreased fluid stress and stress gradients on the flexible wall comparing to that on rigid walls; however, the wall stress gradients are found to be much larger on highly deformable walls with small longitudinal tensions. Therefore, in diseases such as emphysema, with more deformable airways, there is a high possibility of induced injuries on lining cells along the airways because of larger wall stresses and stress gradients.
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Affiliation(s)
- Y Zheng
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2099, USA
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Huh D, Kuo CH, Grotberg JB, Takayama S. Gas-liquid two-phase flow patterns in rectangular polymeric microchannels: effect of surface wetting properties. New J Phys 2009; 11:75034. [PMID: 20126421 PMCID: PMC2814430 DOI: 10.1088/1367-2630/11/7/075034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Here we map gas-liquid two-phase flow regimes observed in polymeric microchannels with different wetting properties. We utilized video and confocal microscopy to examine two-phase flow patterns produced by parallel injection of air and water through a Y-shaped junction into a rectangular microchannel made of poly(dimethylsiloxane) (PDMS). We observed seven flow regimes in microchannels with hydrophobic walls, whereas only two flow patterns were identified in hydrophilic microchannels. Our study demonstrates that surface wettability has a profound influence on the spatial distribution of air and water moving in microchannels.
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Affiliation(s)
- D Huh
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel Blvd, Ann Arbor, MI 48109-2099, USA
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Cho S, Huh D, Kim B, Lee S, Kwon O, Ahn W, Jheon S. Staple Line Covering Procedure after Thoracoscopic Bullectomy for the Management of Primary Spontaneous Pneumothorax. Thorac Cardiovasc Surg 2008; 56:217-20. [DOI: 10.1055/s-2007-989366] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Sherma J, Bretschneider W, Dittamo M, DiBiase N, Huh D, Schwartz DP. Spectrometric and thin-layer chromatographic quantification of sulfathiazole residues in honey. J Chromatogr A 1989; 463:229-33. [PMID: 2715242 DOI: 10.1016/s0021-9673(01)84477-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- J Sherma
- Department of Chemistry, Lafayette College, Easton, PA 18042
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