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Sun P, Cui M, Jing J, Kong F, Wang S, Tang L, Leng J, Chen K. Deciphering the molecular and cellular atlas of immune cells in septic patients with different bacterial infections. J Transl Med 2023; 21:777. [PMID: 37919720 PMCID: PMC10621118 DOI: 10.1186/s12967-023-04631-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/14/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Sepsis is a life-threatening organ dysfunction caused by abnormal immune responses to various, predominantly bacterial, infections. Different bacterial infections lead to substantial variation in disease manifestation and therapeutic strategies. However, the underlying cellular heterogeneity and mechanisms involved remain poorly understood. METHODS Multiple bulk transcriptome datasets from septic patients with 12 types of bacterial infections were integrated to identify signature genes for each infection. Signature genes were mapped onto an integrated large single-cell RNA (scRNA) dataset from septic patients, to identify subsets of cells associated with different sepsis types, and multiple omics datasets were combined to reveal the underlying molecular mechanisms. In addition, an scRNA dataset and spatial transcriptome data were used to identify signaling pathways in sepsis-related cells. Finally, molecular screening, optimization, and de novo design were conducted to identify potential targeted drugs and compounds. RESULTS We elucidated the cellular heterogeneity among septic patients with different bacterial infections. In Escherichia coli (E. coli) sepsis, 19 signature genes involved in epigenetic regulation and metabolism were identified, of which DRAM1 was demonstrated to promote autophagy and glycolysis in response to E. coli infection. DRAM1 upregulation was confirmed in an independent sepsis cohort. Further, we showed that DRAM1 could maintain survival of a pro-inflammatory monocyte subset, C10_ULK1, which induces systemic inflammation by interacting with other cell subsets via resistin and integrin signaling pathways in blood and kidney tissue, respectively. Finally, retapamulin was identified and optimized as a potential drug for treatment of E. coli sepsis targeting the signature gene, DRAM1, and inhibiting E. coli protein synthesis. Several other targeted drugs were also identified in other types of sepsis, including nystatin targeting C1QA in Neisseria sepsis and dalfopristin targeting CTSD in Streptococcus viridans sepsis. CONCLUSION Our study provides a comprehensive overview of the cellular heterogeneity and underlying mechanisms in septic patients with various bacterial infections, providing insights to inform development of stratified targeted therapies for sepsis.
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Affiliation(s)
- Ping Sun
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China
- Department of Emergency, Affiliated Hospital of Yangzhou University, Yangzhou, 225000, China
| | - Mintian Cui
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China
| | - Jiongjie Jing
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China
| | - Fanyu Kong
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Shixi Wang
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China
| | - Lunxian Tang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Junling Leng
- Department of Emergency, Affiliated Hospital of Yangzhou University, Yangzhou, 225000, China
| | - Kun Chen
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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2
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Elek Z, Losoncz E, Fülep Z, Kovács-Nagy R, Bánlaki Z, Szlobodnyik G, Keszler G, Rónai Z. Persistent sepsis-induced transcriptomic signatures in signaling pathways of peripheral blood leukocytes: A pilot study. Hum Immunol 2023; 84:600-608. [PMID: 37673769 DOI: 10.1016/j.humimm.2023.08.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
Sepsis is a dysregulated immune response to infections that frequently precipitates multiple organ dysfunction and death despite intensive supportive therapy. The aim of the present study was to identify sepsis-induced alterations in the signaling transcriptome of peripheral blood leukocytes that might shed light on the elusive transition from proinflammatory to anti-inflammatory responses and underlie long-term post-sepsis immunosuppression. Peripheral blood leukocytes were collected from subjects (i) with systemic inflammation, (ii) with sepsis in the acute phase and (iii) 6 months after recovery from sepsis, corresponding to progressive stages of the disease. Transcriptomic analysis was performed with the QuantStudio 12K Flex OpenArray Human Signal Transduction Panel analyzing transcripts of 573 genes playing a significant role in signaling. Of them, 145 genes exhibited differential expression in sepsis as compared to systemic inflammation. Pathway analysis revealed enhanced expression levels of genes involved in primary immune responses (proinflammatory cytokines, neutrophil and macrophage activation markers) and signatures characteristic of immunosuppression (increased expression of anti-inflammatory cytokines and proapoptotic genes; diminished expression of T and B cell receptor dependent activating and survival pathways). Importantly, sepsis-induced expression patterns of 39 genes were not normalized by the end of the 6-month follow-up period, indicating expression aberrations persisting long after clinical recovery. Functional analysis of these transcripts revealed downregulation of the antiapoptotic Wnt and mTOR signaling pathways that might explain the post-sepsis immunosuppression commonly seen in sepsis survivors.
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Affiliation(s)
- Zsuzsanna Elek
- Institute of Biochemistry and Molecular Biology, Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Eszter Losoncz
- Department of Anesthesiology and Intensive Therapy, Bács-Kiskun County Teaching Hospital, Kecskemét, Hungary; Doctoral School, Semmelweis University, Budapest, Hungary
| | - Zoltán Fülep
- Department of Anesthesiology and Intensive Therapy, Bács-Kiskun County Teaching Hospital, Kecskemét, Hungary
| | - Réka Kovács-Nagy
- Institute of Biochemistry and Molecular Biology, Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsófia Bánlaki
- Institute of Biochemistry and Molecular Biology, Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Gergely Szlobodnyik
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Gergely Keszler
- Institute of Biochemistry and Molecular Biology, Department of Molecular Biology, Semmelweis University, Budapest, Hungary.
| | - Zsolt Rónai
- Institute of Biochemistry and Molecular Biology, Department of Molecular Biology, Semmelweis University, Budapest, Hungary
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3
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He XL, Chen JY, Feng YL, Song P, Wong YK, Xie LL, Wang C, Zhang Q, Bai YM, Gao P, Luo P, Liu Q, Liao FL, Li ZJ, Jiang Y, Wang JG. Single-cell RNA sequencing deciphers the mechanism of sepsis-induced liver injury and the therapeutic effects of artesunate. Acta Pharmacol Sin 2023; 44:1801-1814. [PMID: 37041228 PMCID: PMC10462669 DOI: 10.1038/s41401-023-01065-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/16/2023] [Indexed: 04/13/2023] Open
Abstract
Liver, as an immune and detoxification organ, represents an important line of defense against bacteria and infection and a vulnerable organ that is easily injured during sepsis. Artesunate (ART) is an anti-malaria agent, that also exhibits broad pharmacological activities including anti-inflammatory, immune-regulation and liver protection. In this study, we investigated the cellular responses in liver to sepsis infection and ART hepatic-protective mechanisms against sepsis. Cecal ligation and puncture (CLP)-induced sepsis model was established in mice. The mice were administered ART (10 mg/kg, i.p.) at 4 h, and sacrificed at 12 h after the surgery. Liver samples were collected for preparing single-cell RNA transcriptome sequencing (scRNA-seq). The scRNA-seq analysis revealed that sepsis-induced a dramatic reduction of hepatic endothelial cells, especially the subtypes characterized with proliferation and differentiation. Macrophages were recruited during sepsis and released inflammatory cytokines (Tnf, Il1b, Il6), chemokines (Ccl6, Cd14), and transcription factor (Nfkb1), resulting in liver inflammatory responses. Massive apoptosis of lymphocytes and abnormal recruitment of neutrophils caused immune dysfunction. ART treatment significantly improved the survival of CLP mice within 96 h, and partially relieved or reversed the above-mentioned pathological features, mitigating the impact of sepsis on liver injury, inflammation, and dysfunction. This study provides comprehensive fundamental proof for the liver protective efficacy of ART against sepsis infection, which would potentially contribute to its clinical translation for sepsis therapy. Single cell transcriptome reveals the changes of various hepatocyte subtypes of CLP-induced liver injury and the potential pharmacological effects of artesunate on sepsis.
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Affiliation(s)
- Xue-Ling He
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Jia-Yun Chen
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Yu-Lin Feng
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Ping Song
- China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Lu-Lin Xie
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Chen Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qian Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yun-Meng Bai
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Peng Gao
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Piao Luo
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qiang Liu
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, and Cardiovascular Pharmacology Division of Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, 94304, USA
| | - Fu-Long Liao
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhi-Jie Li
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China.
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Ji-Gang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China.
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China.
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4
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Chen J, He X, Bai Y, Liu J, Wong YK, Xie L, Zhang Q, Luo P, Gao P, Gu L, Guo Q, Cheng G, Wang C, Wang J. Single-cell transcriptome analysis reveals the regulatory effects of artesunate on splenic immune cells in polymicrobial sepsis. J Pharm Anal 2023; 13:817-829. [PMID: 37577384 PMCID: PMC10422109 DOI: 10.1016/j.jpha.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023] Open
Abstract
Sepsis is characterized by a severe and life-threatening host immune response to polymicrobial infection accompanied by organ dysfunction. Studies on the therapeutic effect and mechanism of immunomodulatory drugs on the sepsis-induced hyperinflammatory or immunosuppression states of various immune cells remain limited. This study aimed to investigate the protective effects and underlying mechanism of artesunate (ART) on the splenic microenvironment of cecal ligation and puncture-induced sepsis model mice using single-cell RNA sequencing (scRNA-seq) and experimental validations. The scRNA-seq analysis revealed that ART inhibited the activation of pro-inflammatory macrophages recruited during sepsis. ART could restore neutrophils' chemotaxis and immune function in the septic spleen. It inhibited the activation of T regulatory cells but promoted the cytotoxic function of natural killer cells during sepsis. ART also promoted the differentiation and activity of splenic B cells in mice with sepsis. These results indicated that ART could alleviate the inflammatory and/or immunosuppressive states of various immune cells involved in sepsis to balance the immune homeostasis within the host. Overall, this study provided a comprehensive investigation of the regulatory effect of ART on the splenic microenvironment in sepsis, thus contributing to the application of ART as adjunctive therapy for the clinical treatment of sepsis.
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Affiliation(s)
- Jiayun Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
| | - Xueling He
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yunmeng Bai
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
| | - Jing Liu
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
| | - Yin Kwan Wong
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, 518020, China
| | - Lulin Xie
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
| | - Qian Zhang
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
| | - Piao Luo
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
| | - Peng Gao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liwei Gu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qiuyan Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Guangqing Cheng
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Chen Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jigang Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518020, China
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5
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Dahmer M, Jennings A, Parker M, Sanchez-Pinto LN, Thompson A, Traube C, Zimmerman JJ. Pediatric Critical Care in the Twenty-first Century and Beyond. Crit Care Clin 2023; 39:407-425. [PMID: 36898782 DOI: 10.1016/j.ccc.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pediatric critical care addresses prevention, diagnosis, and treatment of organ dysfunction in the setting of increasingly complex patients, therapies, and environments. Soon burgeoning data science will enable all aspects of intensive care: driving facilitated diagnostics, empowering a learning health-care environment, promoting continuous advancement of care, and informing the continuum of critical care outside the intensive care unit preceding and following critical illness/injury. Although novel technology will progressively objectify personalized critical care, humanism, practiced at the bedside, defines the essence of pediatric critical care now and in the future.
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Affiliation(s)
- Mary Dahmer
- Division of Critical Care, Department of Pediatrics, University of Michigan, 1500 East Medical Center Drive, F6790/5243, Ann Arbor, MI, USA
| | - Aimee Jennings
- Division of Critical Care Medicine, Advanced Practice, FA.2.112, Seattle Children's Hospital, 4800 Sandpoint Way Northeast, Seattle, WA 98105, USA
| | - Margaret Parker
- Department of Pediatrics, Stony Brook University, 7762 Bloomfield Road, Easton, MD 21601, USA
| | - Lazaro N Sanchez-Pinto
- Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, 225 East Chicago Avenue, Box 73, Chicago, IL 60611-2605, USA
| | - Ann Thompson
- Department of Critical Care Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Chani Traube
- Department of Pediatrics, Weill Cornell Medicine, 525 East 68th Street, Box 225, New York, NY 10065, USA
| | - Jerry J Zimmerman
- Department of Pediatrics, FA.2.300B Seattle Children's Hospital, 4800 Sandpoint Way Northeast, Seattle, WA 98105, USA; Pediatric Critical Care Medicine, Seattle Children's Hospital, Harborview Medical Center, University of Washington, School of Medicine, FA.2.300B, Seattle Children's Hospital, 4800 Sand Point Way Northeast, Seattle, WA 98105, USA.
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6
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Avital G, Kuperwaser F, Pountain AW, Lacey KA, Zwack EE, Podkowik M, Shopsin B, Torres VJ, Yanai I. The tempo and mode of gene regulatory programs during bacterial infection. Cell Rep 2022; 41:111477. [PMID: 36223751 PMCID: PMC9741813 DOI: 10.1016/j.celrep.2022.111477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 06/10/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022] Open
Abstract
Innate immune recognition of bacterial pathogens is a key determinant of the ensuing systemic response, and host or pathogen heterogeneity in this early interaction can impact the course of infection. To gain insight into host response heterogeneity, we investigate macrophage inflammatory dynamics using primary human macrophages infected with Group B Streptococcus. Transcriptomic analysis reveals discrete cellular states within responding macrophages, one of which consists of four sub-states, reflecting inflammatory activation. Infection with six additional bacterial species-Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis, Yersinia pseudotuberculosis, Shigella flexneri, and Salmonella enterica-recapitulates these states, though at different frequencies. We show that modulating the duration of infection and the presence of a toxin impacts inflammatory trajectory dynamics. We provide evidence for this trajectory in infected macrophages in an in vivo model of Staphylococcus aureus infection. Our cell-state analysis defines a framework for understanding inflammatory activation dynamics in response to bacterial infection.
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Affiliation(s)
- Gal Avital
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA,These authors contributed equally
| | - Felicia Kuperwaser
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA,These authors contributed equally
| | - Andrew W. Pountain
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Keenan A. Lacey
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Erin E. Zwack
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - Bo Shopsin
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA,Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - Victor J. Torres
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA,Lead contact,Correspondence:
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7
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Manohar M, Jones EK, Rubin SJS, Subrahmanyam PB, Swaminathan G, Mikhail D, Bai L, Singh G, Wei Y, Sharma V, Siebert JC, Maecker HT, Husain SZ, Park WG, Pandol SJ, Habtezion A. Novel Circulating and Tissue Monocytes as Well as Macrophages in Pancreatitis and Recovery. Gastroenterology 2021; 161:2014-2029.e14. [PMID: 34450180 PMCID: PMC8796698 DOI: 10.1053/j.gastro.2021.08.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/28/2021] [Accepted: 08/17/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Acute pancreatitis (AP) is an inflammatory disease with mild to severe course that is associated with local and systemic complications and significant mortality. Uncovering inflammatory pathways that lead to progression and recovery will inform ways to monitor and/or develop effective therapies. METHODS We performed single-cell mass Cytometry by Time Of Flight (CyTOF) analysis to identify pancreatic and systemic inflammatory signals during mild AP (referred to as AP), severe AP (SAP), and recovery using 2 independent experimental models and blood from patients with AP and recurrent AP. Flow cytometric validation of monocytes subsets identified using CyTOF analysis was performed independently. RESULTS Ly6C+ inflammatory monocytes were the most altered cells in the pancreas during experimental AP, recovery, and SAP. Deep profiling uncovered heterogeneity among pancreatic and blood monocytes and identified 7 novel subsets during AP and recovery, and 6 monocyte subsets during SAP. Notably, a dynamic shift in pancreatic CD206+ macrophage population was observed during AP and recovery. Deeper profiling of the CD206+ macrophage identified 7 novel subsets during AP, recovery, and SAP. Differential expression analysis of these novel monocyte and CD206+ macrophage subsets revealed significantly altered surface (CD44, CD54, CD115, CD140a, CD196, podoplanin) and functional markers (interferon-γ, interleukin 4, interleukin 22, latency associated peptide-transforming growth factor-β, tumor necrosis factor-α, T-bet, RoRγt) that were associated with recovery and SAP. Moreover, a targeted functional analysis further revealed distinct expression of pro- and anti-inflammatory cytokines by pancreatic CD206+ macrophage subsets as the disease either progressed or resolved. Similarly, we identified heterogeneity among circulating classical inflammatory monocytes (CD14+CD16-) and novel subsets in patients with AP and recurrent AP. CONCLUSIONS We identified several novel monocyte/macrophage subsets with unique phenotype and functional characteristics that are associated with AP, recovery, and SAP. Our findings highlight differential innate immune responses during AP progression and recovery that can be leveraged for future disease monitoring and targeting.
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Affiliation(s)
- Murli Manohar
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California; Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California.
| | - Elaina K Jones
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California; Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Samuel J S Rubin
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Priyanka B Subrahmanyam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California
| | - Gayathri Swaminathan
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - David Mikhail
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Lawrence Bai
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Gulshan Singh
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Yi Wei
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Vishal Sharma
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California
| | - Sohail Z Husain
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Walter G Park
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Stephen J Pandol
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Aida Habtezion
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California.
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8
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Schuurman AR, Reijnders TDY, Kullberg RFJ, Butler JM, van der Poll T, Wiersinga WJ. Sepsis: deriving biological meaning and clinical applications from high-dimensional data. Intensive Care Med Exp 2021; 9:27. [PMID: 33961170 PMCID: PMC8105470 DOI: 10.1186/s40635-021-00383-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
The pathophysiology of sepsis is multi-facetted and highly complex. As sepsis is a leading cause of global mortality that still lacks targeted therapies, increased understanding of its pathogenesis is vital for improving clinical care and outcomes. An increasing number of investigations seeks to unravel the complexity of sepsis through high-dimensional data analysis, enabled by advances in -omics technologies. Here, we summarize progress in the following major -omics fields: genomics, epigenomics, transcriptomics, proteomics, lipidomics, and microbiomics. We describe what these fields can teach us about sepsis, and highlight current trends and future challenges. Finally, we focus on multi-omics integration, and discuss the challenges in deriving biological meaning and clinical applications from these types of data.
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Affiliation(s)
- Alex R Schuurman
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Tom D Y Reijnders
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Robert F J Kullberg
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Joe M Butler
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands. .,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.
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9
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Yamada Y, Takai S, Watanabe Y, Osaki A, Kawabata Y, Oike A, Hirayama A, Iwata S, Sanematsu K, Tabata S, Shigemura N. Gene expression profiling of α-gustducin-expressing taste cells in mouse fungiform and circumvallate papillae. Biochem Biophys Res Commun 2021; 557:206-212. [PMID: 33872990 DOI: 10.1016/j.bbrc.2021.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 11/27/2022]
Abstract
Taste buds are complex sensory organs embedded in the epithelium of fungiform papillae (FP) and circumvallate papillae (CV). The sweet, bitter, and umami tastes are sensed by type II taste cells that express taste receptors (Tas1rs and Tas2rs) coupled with the taste G-protein α-gustducin. Recent studies revealed that the taste response profiles of α-gustducin-expressing cells are different between FP and CV, but which genes could generate such distinctive cell characteristics are still largely unknown. We performed a comprehensive transcriptome analysis on α-gustducin-expressing cells in mouse FP and CV by single-cell RNA sequencing combined with fluorescence-activated cell sorting. Transcriptome profiles of the α-gustducin-expressing cells showed various expression patterns of taste receptors. Our clustering analysis defined the specific cell populations derived from FP or CV based on their distinct gene expression. Immunohistochemistry confirmed the specific expression of galectin-3, encoded by Lgals3, which was recognized as a differentially expressed gene in the transcriptome analysis. Our work provides fundamental knowledge toward understanding the genetic heterogeneity of type II cells, potentially revealing differential characterization of FP and CV taste bud cells.
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Affiliation(s)
- Yu Yamada
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Laboratory of Functional Anatomy, Graduate School of Biosource and Bioenvironmental Science, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan
| | - Shingo Takai
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan.
| | - Yu Watanabe
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Section of Implant and Rehabilitative Dentistry, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan
| | - Ayana Osaki
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Section of Interdisciplinary Dentistry, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, 812-8582, Fukuoka, Japan
| | - Yuko Kawabata
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan
| | - Asami Oike
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Section of Interdisciplinary Dentistry, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, 812-8582, Fukuoka, Japan
| | - Ayaka Hirayama
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Section of Orthodontics and Dentofacial Orthopedics, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan
| | - Shusuke Iwata
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, 744, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan
| | - Keisuke Sanematsu
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; OBT Research Center, Graduate School of Dental Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, 744, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan
| | - Shoji Tabata
- Laboratory of Functional Anatomy, Graduate School of Biosource and Bioenvironmental Science, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan
| | - Noriatsu Shigemura
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan; Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, 744, Nishi-ku, Fukuoka-city, Fukuoka, 819-0395, Japan.
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10
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Wang T, Zhang X, Liu Z, Yao T, Zheng D, Gan J, Yu S, Li L, Chen P, Sun J. Single-cell RNA sequencing reveals the sustained immune cell dysfunction in the pathogenesis of sepsis secondary to bacterial pneumonia. Genomics 2021; 113:1219-1233. [PMID: 33691144 PMCID: PMC7937330 DOI: 10.1016/j.ygeno.2021.01.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/02/2021] [Accepted: 01/11/2021] [Indexed: 12/29/2022]
Abstract
Sepsis is a leading cause of mortality in intensive care unit worldwide, it's accompanied by immune cell dysfunction induced by multiple factors. However, little is known about the specific alterations in immune cells in the dynamic pathogenesis of sepsis secondary to bacterial pneumonia. Here, we used single cell RNA sequencing (scRNA-seq) to profile peripheral blood mononuclear cells (PBMCs) in a healthy control and two patients with sepsis secondary to bacterial pneumonia, including acute, stable and recovery stage. We analyzed the quantity and function of immune cells. During disease course, interferon gamma response was upregulated; T/NK cell subtypes presented activation and exhaustion properties, which might be driven by monocytes through IL-1β signaling pathways; The proportion of plasma cells was increased, which might be driven by NK cells through IFN signaling pathways; Additionally, interferon gamma response was upregulated to a greater degree in sepsis secondary to pneumonia induced by SARS-COV-2 compared with that induced by influenza virus and bacteria.
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MESH Headings
- Aged
- COVID-19/complications
- COVID-19/genetics
- COVID-19/immunology
- Case-Control Studies
- Cells, Cultured
- Female
- Humans
- Influenza, Human/complications
- Influenza, Human/genetics
- Influenza, Human/immunology
- Leukocytes/immunology
- Leukocytes/metabolism
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Male
- Middle Aged
- Monocytes/immunology
- Monocytes/metabolism
- Pneumonia, Bacterial/complications
- Pneumonia, Bacterial/genetics
- Pneumonia, Bacterial/immunology
- RNA-Seq
- SARS-CoV-2/immunology
- Sepsis/genetics
- Sepsis/immunology
- Sepsis/microbiology
- Sepsis/virology
- Sequence Analysis, RNA/methods
- Single-Cell Analysis/methods
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Affiliation(s)
- Teng Wang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xianglong Zhang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhanguo Liu
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Tong Yao
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dongying Zheng
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jianwei Gan
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Shuang Yu
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Lin Li
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Peng Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Jian Sun
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
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11
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Fu MS, Drummond RA. The Diverse Roles of Monocytes in Cryptococcosis. J Fungi (Basel) 2020; 6:jof6030111. [PMID: 32708673 PMCID: PMC7558978 DOI: 10.3390/jof6030111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023] Open
Abstract
Monocytes are considered to play a central role in the pathogenesis of Cryptococcus neoformans infection. Monocytes and monocyte-derived macrophages and dendritic cells are key components for the control of infection, but paradoxically they can also contribute to detrimental host responses and may even support fungal proliferation and dissemination. Simultaneously, the C. neoformans polysaccharide capsule can impair the functions of monocytes. Although monocytes are often seen as simple precursor cells, they also function as independent immune effector cells. In this review, we summarize these monocyte-specific functions during cryptococcal infection and the influence of C. neoformans on monocyte responses. We also cover the most recent findings on the functional and phenotypic heterogeneity of monocytes and discuss how new advanced technologies provide a platform to address outstanding questions in the field.
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