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Giroux NS, Ding S, McClain MT, Burke TW, Petzold E, Chung HA, Rivera GO, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, De Ussel MI, Satterwhite LL, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Shen X, Woods CW. Author Correction: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion. Sci Rep 2023; 13:6462. [PMID: 37081034 PMCID: PMC10116442 DOI: 10.1038/s41598-023-33323-8] [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: 04/22/2023] Open
Affiliation(s)
- Nicholas S Giroux
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC, 27705, USA
- Division of Infectious Diseases, School of Medicine, Duke University Medical Center, 40 Duke Medicine Circle, Durham, NC, 27710-4000, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Hong A Chung
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Grecia O Rivera
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Ergang Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Rui Xi
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Shree Bose
- Department of Pharmacology and Cancer Biology, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Tomer Rotstein
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | | | - Tianyi Chen
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute and Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute and Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Maria Iglesias De Ussel
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Lisa L Satterwhite
- Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Bryan D Kraft
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC, 27705, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC, 27705, USA
- Division of Infectious Diseases, School of Medicine, Duke University Medical Center, 40 Duke Medicine Circle, Durham, NC, 27710-4000, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
- Durham Veterans Affairs Health Care System, Durham, NC, 27705, USA.
- Division of Infectious Diseases, School of Medicine, Duke University Medical Center, 40 Duke Medicine Circle, Durham, NC, 27710-4000, USA.
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2
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Wang Z, Boretto M, Millen R, Natesh N, Reckzeh ES, Hsu C, Negrete M, Yao H, Quayle W, Heaton BE, Harding AT, Bose S, Driehuis E, Beumer J, Rivera GO, van Ineveld RL, Gex D, DeVilla J, Wang D, Puschhof J, Geurts MH, Yeung A, Hamele C, Smith A, Bankaitis E, Xiang K, Ding S, Nelson D, Delubac D, Rios A, Abi-Hachem R, Jang D, Goldstein BJ, Glass C, Heaton NS, Hsu D, Clevers H, Shen X. Rapid tissue prototyping with micro-organospheres. Stem Cell Reports 2022; 17:1959-1975. [PMID: 35985334 PMCID: PMC9481922 DOI: 10.1016/j.stemcr.2022.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 06/22/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 12/22/2022] Open
Abstract
In vitro tissue models hold great promise for modeling diseases and drug responses. Here, we used emulsion microfluidics to form micro-organospheres (MOSs), which are droplet-encapsulated miniature three-dimensional (3D) tissue models that can be established rapidly from patient tissues or cells. MOSs retain key biological features and responses to chemo-, targeted, and radiation therapies compared with organoids. The small size and large surface-to-volume ratio of MOSs enable various applications including quantitative assessment of nutrient dependence, pathogen-host interaction for anti-viral drug screening, and a rapid potency assay for chimeric antigen receptor (CAR)-T therapy. An automated MOS imaging pipeline combined with machine learning overcomes plating variation, distinguishes tumorspheres from stroma, differentiates cytostatic versus cytotoxic drug effects, and captures resistant clones and heterogeneity in drug response. This pipeline is capable of robust assessments of drug response at individual-tumorsphere resolution and provides a rapid and high-throughput therapeutic profiling platform for precision medicine.
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Affiliation(s)
- Zhaohui Wang
- Woo Center for Big Data and Precision Health, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Matteo Boretto
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Rosemary Millen
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Naveen Natesh
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Elena S Reckzeh
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Carolyn Hsu
- College of Arts and Sciences, University of Chapel Hill, Chapel Hill, NC, USA
| | - Marcos Negrete
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Haipei Yao
- Biology Department, Trinity School of Arts and Sciences, Duke University, Durham, NC, USA
| | | | - Brook E Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - Shree Bose
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Else Driehuis
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Joep Beumer
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Grecia O Rivera
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 Utrecht, the Netherlands
| | | | | | - Daisong Wang
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jens Puschhof
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Maarten H Geurts
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Athena Yeung
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Cait Hamele
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | | | | | - Kun Xiang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA; Xilis, Inc., Durham, NC, USA
| | | | | | - Anne Rios
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 Utrecht, the Netherlands
| | - Ralph Abi-Hachem
- Department of Head and Neck Surgery and Communication Sciences, School of Medicine, Duke University, Durham, NC, USA
| | - David Jang
- Department of Head and Neck Surgery and Communication Sciences, School of Medicine, Duke University, Durham, NC, USA
| | - Bradley J Goldstein
- Department of Head and Neck Surgery and Communication Sciences, School of Medicine, Duke University, Durham, NC, USA
| | - Carolyn Glass
- Department of Pathology, School of Medicine, Duke University, Durham, NC, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - David Hsu
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, USA.
| | - Hans Clevers
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 Utrecht, the Netherlands.
| | - Xiling Shen
- Woo Center for Big Data and Precision Health, Pratt School of Engineering, Duke University, Durham, NC, USA; Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA; Terasaki Institute, Los Angeles, CA, USA.
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3
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Bose S, Huang Q, Ma Y, Wang L, Rivera GO, Ouyang Y, Whitaker R, Gibson RA, Kontos CD, Berchuck A, Previs RA, Shen X. G6PD inhibition sensitizes ovarian cancer cells to oxidative stress in the metastatic omental microenvironment. Cell Rep 2022; 39:111012. [PMID: 35767962 PMCID: PMC9534522 DOI: 10.1016/j.celrep.2022.111012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 11/22/2021] [Revised: 04/17/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecological malignancy, with aggressive metastatic disease responsible for the majority of OC-related deaths. In particular, OC tumors preferentially metastasize to and proliferate rapidly in the omentum. Here, we show that metastatic OC cells experience increased oxidative stress in the omental microenvironment. Metabolic reprogramming, including upregulation of the pentose phosphate pathway (PPP), a key cellular redox homeostasis mechanism, allows OC cells to compensate for this challenge. Inhibition of glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the PPP, reduces tumor burden in pre-clinical models of OC, suggesting that this adaptive metabolic dependency is important for OC omental metastasis. Bose et al. characterize the importance of G6PD, the rate-limiting enzyme of the oxidative pentose phosphate pathway, in mitigating oxidative stress experienced by ovarian cancer cells metastasizing to the omentum.
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Affiliation(s)
- Shree Bose
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Qiang Huang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710006, China
| | - Yunhan Ma
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Lihua Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Grecia O Rivera
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Yunxin Ouyang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Regina Whitaker
- Division of Gynecological Oncology, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27708, USA
| | - Rebecca A Gibson
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Christopher D Kontos
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27708, USA; Department of Medicine, Division of Cardiology, Duke University Medical Center, Durham, NC 27708, USA
| | - Andrew Berchuck
- Division of Gynecological Oncology, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27708, USA
| | - Rebecca A Previs
- Division of Gynecological Oncology, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27708, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA.
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4
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Ding S, Hsu C, Wang Z, Natesh NR, Millen R, Negrete M, Giroux N, Rivera GO, Dohlman A, Bose S, Rotstein T, Spiller K, Yeung A, Sun Z, Jiang C, Xi R, Wilkin B, Randon PM, Williamson I, Nelson DA, Delubac D, Oh S, Rupprecht G, Isaacs J, Jia J, Chen C, Shen JP, Kopetz S, McCall S, Smith A, Gjorevski N, Walz AC, Antonia S, Marrer-Berger E, Clevers H, Hsu D, Shen X. Patient-derived micro-organospheres enable clinical precision oncology. Cell Stem Cell 2022; 29:905-917.e6. [PMID: 35508177 PMCID: PMC9177814 DOI: 10.1016/j.stem.2022.04.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [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: 09/16/2021] [Revised: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 02/09/2023]
Abstract
Patient-derived xenografts (PDXs) and patient-derived organoids (PDOs) have been shown to model clinical response to cancer therapy. However, it remains challenging to use these models to guide timely clinical decisions for cancer patients. Here, we used droplet emulsion microfluidics with temperature control and dead-volume minimization to rapidly generate thousands of micro-organospheres (MOSs) from low-volume patient tissues, which serve as an ideal patient-derived model for clinical precision oncology. A clinical study of recently diagnosed metastatic colorectal cancer (CRC) patients using an MOS-based precision oncology pipeline reliably assessed tumor drug response within 14 days, a timeline suitable for guiding treatment decisions in the clinic. Furthermore, MOSs capture original stromal cells and allow T cell penetration, providing a clinical assay for testing immuno-oncology (IO) therapies such as PD-1 blockade, bispecific antibodies, and T cell therapies on patient tumors.
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Affiliation(s)
- Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Xilis, Inc., Durham, NC 27713, USA
| | - Carolyn Hsu
- College of Arts and Sciences, University of Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhaohui Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Xilis, Inc., Durham, NC 27713, USA
| | - Naveen R Natesh
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Rosemary Millen
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Marcos Negrete
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Nicholas Giroux
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Grecia O Rivera
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Anders Dohlman
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Shree Bose
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Tomer Rotstein
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | | | - Athena Yeung
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Zhiguo Sun
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Chongming Jiang
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rui Xi
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | | | - Peggy M Randon
- National Institute of Environmental Health Sciences (NIEHS), Durham, NC 27709, USA
| | - Ian Williamson
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | | | | | - Sehwa Oh
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Gabrielle Rupprecht
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - James Isaacs
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Jingquan Jia
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Chao Chen
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, MD Anderson, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, MD Anderson, Houston, TX 77030, USA
| | - Shannon McCall
- Department of Pathology, Duke University, Durham, NC 27708, USA
| | | | - Nikolche Gjorevski
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center, Basel 4058, Switzerland
| | - Antje-Christine Walz
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center, Basel 4058, Switzerland
| | - Scott Antonia
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Estelle Marrer-Berger
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center, Basel 4058, Switzerland
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Roche Pharmaceutical Research and Early Development, Roche Innovation Center, Basel 4058, Switzerland.
| | - David Hsu
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27708, USA.
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA.
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5
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Giroux NS, Ding S, Mcclain MT, Burke TW, Petzold E, Chung HA, Rivera GO, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, De Ussel MI, Satterwhite LL, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Shen X, Woods C. Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion.. [PMID: 35411343 PMCID: PMC8996625 DOI: 10.21203/rs.3.rs-1479864/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Abstract
SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associate with mild or moderate symptoms are already robust and include severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity is marked by upregulation classical antiviral pathways including those regulating IRF1 and IRF7, whereas in moderate disease these classical antiviral signals diminish suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.
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6
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Yu C, Littleton S, Giroux NS, Mathew R, Ding S, Kalnitsky J, Yang Y, Petzold E, Chung HA, Rivera GO, Rotstein T, Xi R, Ko ER, Tsalik EL, Sempowski GD, Denny TN, Burke TW, McClain MT, Woods CW, Shen X, Saban DR. Mucosal-associated invariant T cell responses differ by sex in COVID-19. Med 2021; 2:755-772.e5. [PMID: 33870241 PMCID: PMC8043578 DOI: 10.1016/j.medj.2021.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 12/22/2020] [Revised: 02/09/2021] [Accepted: 04/07/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Sexual dimorphisms in immune responses contribute to coronavirus disease 2019 (COVID-19) outcomes, but the mechanisms governing this disparity remain incompletely understood. METHODS We carried out sex-balanced sampling of peripheral blood mononuclear cells from hospitalized and non-hospitalized individuals with confirmed COVID-19, uninfected close contacts, and healthy control individuals for 36-color flow cytometry and single-cell RNA sequencing. FINDINGS Our results revealed a pronounced reduction of circulating mucosal-associated invariant T (MAIT) cells in infected females. Integration of published COVID-19 airway tissue datasets suggests that this reduction represented a major wave of MAIT cell extravasation during early infection in females. Moreover, MAIT cells from females possessed an immunologically active gene signature, whereas cells from males were pro-apoptotic. CONCLUSIONS Our findings uncover a female-specific protective MAIT cell profile, potentially shedding light on reduced COVID-19 susceptibility in females. FUNDING This work was supported by NIH/NIAID (U01AI066569 and UM1AI104681), the Defense Advanced Projects Agency (DARPA; N66001-09-C-2082 and HR0011-17-2-0069), the Veterans Affairs Health System, and Virology Quality Assurance (VQA; 75N93019C00015). The content is solely the responsibility of the authors and does not necessarily represent the official view of the National Institutes of Health. COVID-19 samples were processed under Biosafety level 2 (BSL-2) with aerosol management enhancement or BSL-3 in the Duke Regional Biocontainment Laboratory, which received partial support for construction from NIH/NIAID (UC6AI058607).
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Affiliation(s)
- Chen Yu
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sejiro Littleton
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas S Giroux
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27710, USA
| | - Rose Mathew
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27710, USA
| | - Joan Kalnitsky
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27710, USA
| | - Hong A Chung
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27710, USA
| | - Grecia O Rivera
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27710, USA
| | - Tomer Rotstein
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27710, USA
| | - Rui Xi
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27710, USA
- Duke Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27710, USA
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27710, USA
| | - Daniel R Saban
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
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