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Gibbs KD, Wang L, Yang Z, Anderson CE, Bourgeois JS, Cao Y, Gaggioli MR, Biel M, Puertollano R, Chen CC, Ko DC. Human variation impacting MCOLN2 restricts Salmonella Typhi replication by magnesium deprivation. Cell Genom 2023; 3:100290. [PMID: 37228749 PMCID: PMC10203047 DOI: 10.1016/j.xgen.2023.100290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 05/27/2023]
Abstract
Human genetic diversity can reveal critical factors in host-pathogen interactions. This is especially useful for human-restricted pathogens like Salmonella enterica serovar Typhi (S. Typhi), the cause of typhoid fever. One key defense during bacterial infection is nutritional immunity: host cells attempt to restrict bacterial replication by denying bacteria access to key nutrients or supplying toxic metabolites. Here, a cellular genome-wide association study of intracellular replication by S. Typhi in nearly a thousand cell lines from around the world-and extensive follow-up using intracellular S. Typhi transcriptomics and manipulation of magnesium availability-demonstrates that the divalent cation channel mucolipin-2 (MCOLN2 or TRPML2) restricts S. Typhi intracellular replication through magnesium deprivation. Mg2+ currents, conducted through MCOLN2 and out of endolysosomes, were measured directly using patch-clamping of the endolysosomal membrane. Our results reveal Mg2+ limitation as a key component of nutritional immunity against S. Typhi and as a source of variable host resistance.
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Affiliation(s)
- Kyle D. Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Zhuo Yang
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Caroline E. Anderson
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Jeffrey S. Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Yanlu Cao
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Margaret R. Gaggioli
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Martin Biel
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rosa Puertollano
- Cell and Developmental Biology Center, National Heart, Lung, & Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Cheng-Chang Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
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2
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Phelan JP, Bourgeois JS, McCarthy JE, Hu LT. A putative xanthine dehydrogenase is critical for Borrelia burgdorferi survival in ticks and mice. Microbiology (Reading) 2023; 169:001286. [PMID: 36748545 PMCID: PMC9993122 DOI: 10.1099/mic.0.001286] [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] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Borrelia burgdorferi is a pathogenic bacterium and the causative agent of Lyme disease. It is exposed to reactive oxygen species (ROS) in both the vertebrate and tick hosts. While some mechanisms by which B. burgdorferi ameliorates the effects of ROS exposure have been studied, there are likely other unknown mechanisms of ROS neutralization that contribute to virulence. Here, we follow up on a three gene cluster of unknown function, bb_0554, bb_0555, and bb_0556, that our prior unbiased transposon insertional sequencing studies implicated in both ROS survival and survival in Ixodes scapularis. We confirmed these findings through genetic knockout and provide evidence that these genes are co-transcribed as an operon to produce a xanthine dehydrogenase. In agreement with these results, we found that B. burgdorferi exposure to either uric acid (a product of xanthine dehydrogenase) or allopurinol (an inhibitor of xanthine dehydrogenase) could modulate sensitivity to ROS in a bb_0554-bb_0556 dependent manner. Together, this study identifies a previously uncharacterized three gene operon in B. burgdorferi as encoding a putative xanthine dehydrogenase critical for virulence. We propose renaming this locus xdhACB.
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Affiliation(s)
- James P Phelan
- Tufts University, Department of Molecular Biology and Microbiology, Boston, Massachusetts, USA.,Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
| | - Jeffrey S Bourgeois
- Tufts University, Department of Molecular Biology and Microbiology, Boston, Massachusetts, USA.,Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
| | - Julie E McCarthy
- Tufts University, Department of Molecular Biology and Microbiology, Boston, Massachusetts, USA.,Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
| | - Linden T Hu
- Tufts University, Department of Molecular Biology and Microbiology, Boston, Massachusetts, USA.,Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
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3
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Schott BH, Wang L, Zhu X, Harding AT, Ko ER, Bourgeois JS, Washington EJ, Burke TW, Anderson J, Bergstrom E, Gardener Z, Paterson S, Brennan RG, Chiu C, McClain MT, Woods CW, Gregory SG, Heaton NS, Ko DC. Single-cell genome-wide association reveals that a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus. Cell Genom 2022; 2:100207. [PMID: 36465279 PMCID: PMC9718543 DOI: 10.1016/j.xgen.2022.100207] [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] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/26/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
During pandemics, individuals exhibit differences in risk and clinical outcomes. Here, we developed single-cell high-throughput human in vitro susceptibility testing (scHi-HOST), a method for rapidly identifying genetic variants that confer resistance and susceptibility. We applied this method to influenza A virus (IAV), the cause of four pandemics since the start of the 20th century. scHi-HOST leverages single-cell RNA sequencing (scRNA-seq) to simultaneously assign genetic identity to cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral burden, and identify expression quantitative trait loci. Integration of scHi-HOST with human challenge and experimental validation demonstrated that a missense variant in endoplasmic reticulum aminopeptidase 1 (ERAP1; rs27895) increased IAV burden in cells and human volunteers. rs27895 exhibits population differentiation, likely contributing to greater permissivity of cells from African populations to IAV. scHi-HOST is a broadly applicable method and resource for decoding infectious-disease genetics.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- These authors contributed equally
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- These authors contributed equally
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Hospital Medicine, Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Durham, NC 27705, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Jack Anderson
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Emma Bergstrom
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Zoe Gardener
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Suzanna Paterson
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Lead contact
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Bourgeois JS, Smith CM, Ko DC. These Are the Genes You're Looking For: Finding Host Resistance Genes. Trends Microbiol 2021; 29:346-362. [PMID: 33004258 PMCID: PMC7969353 DOI: 10.1016/j.tim.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/13/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Humanity's ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host-pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial infection. Here we discuss current trends in defining host-bacterial interactions at the genome-wide level, including screens that harness CRISPR/Cas9 genome editing, natural genetic variation, proteomics, and transcriptomics. We report on the merits, limitations, and findings of these innovative screens and discuss their complementary nature. Finally, we speculate on future innovation as we continue to progress through the postgenomic era and towards deeper mechanistic insight and clinical applications.
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Affiliation(s)
- Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Duke Human Vaccine Institute, School of Medicine, Duke University Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA.
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5
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Perez-Diez A, Wong CS, Liu X, Mystakelis H, Song J, Lu Y, Sheikh V, Bourgeois JS, Lisco A, Laidlaw E, Cudrici C, Zhu C, Li QZ, Freeman AF, Williamson PR, Anderson M, Roby G, Tsang JS, Siegel R, Sereti I. Prevalence and pathogenicity of autoantibodies in patients with idiopathic CD4 lymphopenia. J Clin Invest 2021; 130:5326-5337. [PMID: 32634122 DOI: 10.1172/jci136254] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 01/07/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUNDIdiopathic CD4 lymphopenia (ICL) is defined by persistently low CD4+ cell counts (<300 cells/μL) in the absence of a causal infection or immune deficiency and can manifest with opportunistic infections. Approximately 30% of ICL patients develop autoimmune disease. The prevalence and breadth of their autoantibodies, however, and their potential contribution to pathogenesis of ICL remain unclear.METHODSWe hybridized 34 and 51 ICL patients' sera to a 9,000-human-proteome array and to a 128-known-autoantigen array, respectively. Using a flow-based method, we characterized the presence of anti-lymphocyte Abs in the whole cohort of 72 patients, as well as the Ab functional capability of inducing Ab-dependent cell-mediated cytotoxicity (ADCC), complement deposition, and complement-dependent cytotoxicity (CDC). We tested ex vivo the activation of the classical complement pathway on ICL CD4+ T cells.RESULTSAll ICL patients had a multitude of autoantibodies mostly directed against private (not shared) targets and unrelated quantitatively or qualitatively to the patients' autoimmune disease status. The targets included lymphocyte intracellular and membrane antigens, confirmed by the detection by flow of IgM and IgG (mostly IgG1 and IgG4) anti-CD4+ cell Abs in 50% of the patients, with half of these cases triggering lysis of CD4+ T cells. We also detected in vivo classical complement activation on CD4+ T cells in 14% of the whole cohort.CONCLUSIONOur data demonstrate that a high prevalence of autoantibodies in ICL, some of which are specific for CD4+ T cells, may contribute to pathogenesis, and may represent a potentially novel therapeutic target.TRIAL REGISTRATIONClinicalTrials.gov NCT00867269.FUNDINGNIAID and National Institute of Arthritis and Musculoskeletal and Skin Diseases of the NIH.
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Affiliation(s)
| | - Chun-Shu Wong
- HIV Pathogenesis Section, Laboratory of Immunoregulation, and
| | - Xiangdong Liu
- HIV Pathogenesis Section, Laboratory of Immunoregulation, and
| | | | - Jian Song
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), and
| | - Yong Lu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), and
| | - Virginia Sheikh
- HIV Pathogenesis Section, Laboratory of Immunoregulation, and
| | | | - Andrea Lisco
- HIV Pathogenesis Section, Laboratory of Immunoregulation, and
| | | | - Cornelia Cudrici
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | | | - Quan-Zhen Li
- Microarray Core Facility and.,Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Peter R Williamson
- Translational Mycology Section, Laboratory of Clinical and Molecular Immunology, NIAID, and
| | - Megan Anderson
- HIV Pathogenesis Section, Laboratory of Immunoregulation, and
| | - Gregg Roby
- HIV Pathogenesis Section, Laboratory of Immunoregulation, and
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), and.,Trans-NIH Center for Human Immunology, NIH, Bethesda, Maryland, USA
| | - Richard Siegel
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Irini Sereti
- HIV Pathogenesis Section, Laboratory of Immunoregulation, and
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6
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Gibbs KD, Washington EJ, Jaslow SL, Bourgeois JS, Foster MW, Guo R, Brennan RG, Ko DC. The Salmonella Secreted Effector SarA/SteE Mimics Cytokine Receptor Signaling to Activate STAT3. Cell Host Microbe 2019; 27:129-139.e4. [PMID: 31901521 DOI: 10.1016/j.chom.2019.11.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 08/02/2019] [Revised: 11/05/2019] [Accepted: 11/21/2019] [Indexed: 01/18/2023]
Abstract
Bacteria masterfully co-opt and subvert host signal transduction. As a paradigmatic example, Salmonella uses two type-3 secretion systems to inject effector proteins that facilitate Salmonella entry, establishment of an intracellular niche, and modulation of immune responses. We previously demonstrated that the Salmonella anti-inflammatory response activator SarA (Stm2585, GogC, PagJ, SteE) activates the host transcription factor STAT3 to drive expression of immunomodulatory STAT3-targets. Here, we demonstrate-by sequence, function, and biochemical measurement-that SarA mimics the cytoplasmic domain of glycoprotein 130 (gp130, IL6ST). SarA is phosphorylated at a YxxQ motif, facilitating binding to STAT3 with greater affinity than gp130. Departing from canonical gp130 signaling, SarA function is JAK-independent but requires GSK-3, a key regulator of metabolism and development. Our results reveal that SarA undergoes host phosphorylation to recruit a STAT3-activating complex, circumventing cytokine receptor activation. Effector mimicry of gp130 suggests GSK-3 can regulate normal cytokine signaling, potentially enabling metabolic and immune crosstalk.
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Affiliation(s)
- Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Sarah L Jaslow
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Matthew W Foster
- Duke Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27710, USA
| | - Robyn Guo
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA.
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7
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Bourgeois JS, Jacob J, Garewal A, Ndahayo R, Paxson J. The Bioavailability of Soluble Cigarette Smoke Extract Is Reduced through Interactions with Cells and Affects the Cellular Response to CSE Exposure. PLoS One 2016; 11:e0163182. [PMID: 27649082 PMCID: PMC5029896 DOI: 10.1371/journal.pone.0163182] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/02/2016] [Indexed: 11/26/2022] Open
Abstract
Cellular exposure to cigarette smoke leads to an array of complex responses including apoptosis, cellular senescence, telomere dysfunction, cellular aging, and neoplastic transformation. To study the cellular response to cigarette smoke, a common in vitro model exposes cultured cells to a nominal concentration (i.e. initial concentration) of soluble cigarette smoke extract (CSE). However, we report that use of the nominal concentration of CSE as the only measure of cellular exposure is inadequate. Instead, we demonstrate that cellular response to CSE exposure is dependent not only on the nominal concentration of CSE, but also on specific experimental variables, including the total cell number, and the volume of CSE solution used. As found in other similar xenobiotic assays, our work suggests that the effective dose of CSE is more accurately related to the amount of bioavailable chemicals per cell. In particular, interactions of CSE components both with cells and other physical factors limit CSE bioavailability, as demonstrated by a quantifiably reduced cellular response to CSE that is first modified by such interactions. This has broad implications for the nature of cellular response to CSE exposure, and for the design of in vitro assays using CSE.
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Affiliation(s)
- Jeffrey S. Bourgeois
- Department of Biology, College of the Holy Cross, Worcester, MA, 01610, United States of America
| | - Jeeva Jacob
- Department of Biology, College of the Holy Cross, Worcester, MA, 01610, United States of America
| | - Aram Garewal
- Department of Biology, College of the Holy Cross, Worcester, MA, 01610, United States of America
| | - Renata Ndahayo
- Department of Biology, College of the Holy Cross, Worcester, MA, 01610, United States of America
| | - Julia Paxson
- Department of Biology, College of the Holy Cross, Worcester, MA, 01610, United States of America
- * E-mail:
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