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Nguyen THO, Rowntree LC, Chua BY, Thwaites RS, Kedzierska K. Defining the balance between optimal immunity and immunopathology in influenza virus infection. Nat Rev Immunol 2024:10.1038/s41577-024-01029-1. [PMID: 38698083 DOI: 10.1038/s41577-024-01029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 05/05/2024]
Abstract
Influenza A viruses remain a global threat to human health, with continued pandemic potential. In this Review, we discuss our current understanding of the optimal immune responses that drive recovery from influenza virus infection, highlighting the fine balance between protective immune mechanisms and detrimental immunopathology. We describe the contribution of innate and adaptive immune cells, inflammatory modulators and antibodies to influenza virus-specific immunity, inflammation and immunopathology. We highlight recent human influenza virus challenge studies that advance our understanding of susceptibility to influenza and determinants of symptomatic disease. We also describe studies of influenza virus-specific immunity in high-risk groups following infection and vaccination that inform the design of future vaccines to promote optimal antiviral immunity, particularly in vulnerable populations. Finally, we draw on lessons from the COVID-19 pandemic to refocus our attention to the ever-changing, highly mutable influenza A virus, predicted to cause future global pandemics.
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Affiliation(s)
- Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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Uthappa DM, McClain MT, Nicholson BP, Park LP, Zhbannikov I, Suchindran S, Jimenez M, Constantine FJ, Nichols M, Jones DC, Hudson LL, Jaggers LB, Veldman T, Burke TW, Tsalik EL, Ginsburg GS, Woods CW. Implementation of a Prospective Index-Cluster Sampling Strategy for the Detection of Presymptomatic Viral Respiratory Infection in Undergraduate Students. Open Forum Infect Dis 2024; 11:ofae081. [PMID: 38440301 PMCID: PMC10911223 DOI: 10.1093/ofid/ofae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Background Index-cluster studies may help characterize the spread of communicable infections in the presymptomatic state. We describe a prospective index-cluster sampling strategy (ICSS) to detect presymptomatic respiratory viral illness and its implementation in a college population. Methods We enrolled an annual cohort of first-year undergraduates who completed daily electronic symptom diaries to identify index cases (ICs) with respiratory illness. Investigators then selected 5-10 potentially exposed, asymptomatic close contacts (CCs) who were geographically co-located to follow for infections. Symptoms and nasopharyngeal samples were collected for 5 days. Logistic regression model-based predictions for proportions of self-reported illness were compared graphically for the whole cohort sampling group and the CC group. Results We enrolled 1379 participants between 2009 and 2015, including 288 ICs and 882 CCs. The median number of CCs per IC was 6 (interquartile range, 3-8). Among the 882 CCs, 111 (13%) developed acute respiratory illnesses. Viral etiology testing in 246 ICs (85%) and 719 CCs (82%) identified a pathogen in 57% of ICs and 15% of CCs. Among those with detectable virus, rhinovirus was the most common (IC: 18%; CC: 6%) followed by coxsackievirus/echovirus (IC: 11%; CC: 4%). Among 106 CCs with a detected virus, only 18% had the same virus as their associated IC. Graphically, CCs did not have a higher frequency of self-reported illness relative to the whole cohort sampling group. Conclusions Establishing clusters by geographic proximity did not enrich for cases of viral transmission, suggesting that ICSS may be a less effective strategy to detect spread of respiratory infection.
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Affiliation(s)
- Diya M Uthappa
- Doctor of Medicine Program, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Micah T McClain
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | | | - Lawrence P Park
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Ilya Zhbannikov
- Bioinformatics and Clinical Analytics Team, Clinical Research Unit, Duke University Department of Medicine, Durham, North Carolina, USA
| | - Sunil Suchindran
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Monica Jimenez
- Institute for Medical Research, Durham, North Carolina, USA
| | - Florica J Constantine
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Marshall Nichols
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - Daphne C Jones
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Lori L Hudson
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - L Brett Jaggers
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Timothy Veldman
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Thomas W Burke
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher W Woods
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
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3
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Verma G, Rebholz-Schuhmann D, Madden MG. Enabling personalised disease diagnosis by combining a patient's time-specific gene expression profile with a biomedical knowledge base. BMC Bioinformatics 2024; 25:62. [PMID: 38326757 PMCID: PMC10848462 DOI: 10.1186/s12859-024-05674-0] [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: 12/11/2022] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Recent developments in the domain of biomedical knowledge bases (KBs) open up new ways to exploit biomedical knowledge that is available in the form of KBs. Significant work has been done in the direction of biomedical KB creation and KB completion, specifically, those having gene-disease associations and other related entities. However, the use of such biomedical KBs in combination with patients' temporal clinical data still largely remains unexplored, but has the potential to immensely benefit medical diagnostic decision support systems. RESULTS We propose two new algorithms, LOADDx and SCADDx, to combine a patient's gene expression data with gene-disease association and other related information available in the form of a KB, to assist personalized disease diagnosis. We have tested both of the algorithms on two KBs and on four real-world gene expression datasets of respiratory viral infection caused by Influenza-like viruses of 19 subtypes. We also compare the performance of proposed algorithms with that of five existing state-of-the-art machine learning algorithms (k-NN, Random Forest, XGBoost, Linear SVM, and SVM with RBF Kernel) using two validation approaches: LOOCV and a single internal validation set. Both SCADDx and LOADDx outperform the existing algorithms when evaluated with both validation approaches. SCADDx is able to detect infections with up to 100% accuracy in the cases of Datasets 2 and 3. Overall, SCADDx and LOADDx are able to detect an infection within 72 h of infection with 91.38% and 92.66% average accuracy respectively considering all four datasets, whereas XGBoost, which performed best among the existing machine learning algorithms, can detect the infection with only 86.43% accuracy on an average. CONCLUSIONS We demonstrate how our novel idea of using the most and least differentially expressed genes in combination with a KB can enable identification of the diseases that a patient is most likely to have at a particular time, from a KB with thousands of diseases. Moreover, the proposed algorithms can provide a short ranked list of the most likely diseases for each patient along with their most affected genes, and other entities linked with them in the KB, which can support health care professionals in their decision-making.
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Affiliation(s)
- Ghanshyam Verma
- Insight Centre for Data Analytics, School of Computer Science, University of Galway, Galway, Ireland.
- School of Computer Science, University of Galway, Galway, Ireland.
| | | | - Michael G Madden
- Insight Centre for Data Analytics, School of Computer Science, University of Galway, Galway, Ireland
- School of Computer Science, University of Galway, Galway, Ireland
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Lim FY, Lea HG, Dostie A, van Neel T, Hassan G, Takezawa MG, Starita LM, Adams K, Boeckh M, Schiffer JT, Waghmare A, Berthier E, Theberge AB. homeRNA self-blood collection enables high-frequency temporal profiling of pre-symptomatic host immune kinetics to respiratory viral infection: a prospective cohort study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.12.23296835. [PMID: 37873251 PMCID: PMC10593056 DOI: 10.1101/2023.10.12.23296835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Early host immunity to acute respiratory infections (ARIs) is heterogenous, dynamic, and critical to an individual's infection outcome. Due to limitations in sampling frequency/timepoints, kinetics of early immune dynamics in natural human infections remain poorly understood. In this nationwide prospective cohort study, we leveraged a self-blood collection tool (homeRNA) to profile detailed kinetics of the pre-symptomatic to convalescence host immunity to contemporaneous respiratory pathogens. Methods We enrolled non-symptomatic adults with recent exposure to ARIs who subsequently tested negative (exposed-uninfected) or positive for respiratory pathogens. Participants self-collected blood and nasal swabs daily for seven consecutive days followed by weekly blood collection for up to seven additional weeks. Symptom burden was assessed during each collection. Nasal swabs were tested for SARS-CoV-2 and common respiratory pathogens. 92 longitudinal blood samples spanning the pre-shedding to post-acute phase of eight SARS-CoV-2-infected participants and 40 interval-matched samples from four exposed-uninfected participants were subjected to high-frequency longitudinal profiling of 773 host immune genes. Findings Between June 2021 - April 2022, 68 participants across 26 U.S. states completed the study and self-collected a total of 691 and 466 longitudinal blood and nasal swab samples along with 688 symptom surveys. SARS-CoV-2 was detected in 17 out of 22 individuals with study-confirmed respiratory infection. With rapid dissemination of home self-collection kits, two and four COVID-19+ participants started collection prior to viral shedding and symptom onset, respectively, enabling us to profile detailed expression kinetics of the earliest blood transcriptional response to contemporaneous variants of concern. In pre-shedding samples, we observed transient but robust expression of T-cell response signatures, transcription factor complexes, prostaglandin biosynthesis genes, pyrogenic cytokines, and cytotoxic granule genes. This is followed by a rapid induction of many interferon-stimulated genes (ISGs), concurrent to onset of viral shedding and increase in nasal viral load. Finally, we observed increased expression of host defense peptides (HDPs) in exposed-uninfected individuals over the 4-week observational window. Interpretation We demonstrated that unsupervised self-collection and stabilization of capillary blood can be applied to natural infection studies to characterize detailed early host immune kinetics at a temporal resolution comparable to that of human challenge studies. The remote (decentralized) study framework enables conduct of large-scale population-wide longitudinal mechanistic studies. Expression of cytotoxic/T-cell signatures in pre-shedding samples preceding expansion of innate ISGs suggests a potential role for T-cell mediated pathogen control during early infection. Elevated expression of HDPs in exposed-uninfected individuals warrants further validation studies to assess their potential role in protective immunity during pathogen exposure. Funding This study was funded by R35GM128648 to ABT for in-lab developments of homeRNA, Packard Fellowship from the David and Lucile Packard Foundation to ABT, and R01AI153087 to AW.
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Affiliation(s)
- Fang Yun Lim
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Hannah G. Lea
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
- Department of Therapeutic Radiology, Yale University School of Medicine; New Haven, CT, U.S.A
| | - Ashley Dostie
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Tammi van Neel
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Grant Hassan
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Meg G. Takezawa
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Lea M. Starita
- Brotman Baty Institute, University of Washington; Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington, U.S.A
| | - Karen Adams
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
- Institute of Translational Health Sciences, School of Medicine, University of Washington, Seattle, WA, U.S.A
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
- Department of Medicine, University of Washington; Seattle, Washington, U.S.A
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
- Department of Medicine, University of Washington; Seattle, Washington, U.S.A
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
- Department of Pediatrics, University of Washington; Seattle, Washington, U.S.A
- Seattle Children’s Research Institute; Seattle, Washington, U.S.A
| | - Erwin Berthier
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Ashleigh B. Theberge
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
- Department of Urology, University of Washington; Seattle, Washington, U.S.A
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Galanti M, Patiño-Galindo JA, Filip I, Morita H, Galianese A, Youssef M, Comito D, Ligon C, Lane B, Matienzo N, Ibrahim S, Tagne E, Shittu A, Elliott O, Perea-Chamblee T, Natesan S, Rosenbloom DS, Shaman J, Rabadan R. Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people. PLoS Biol 2024; 22:e3002089. [PMID: 38236818 PMCID: PMC10796020 DOI: 10.1371/journal.pbio.3002089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/22/2023] [Indexed: 01/22/2024] Open
Abstract
Viral respiratory infections are an important public health concern due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup, and bacterial coinfections. To understand these interactions within natural infections, we designed a longitudinal cohort study actively surveilling respiratory viruses over the course of 19 months (2016 to 2018) in a diverse cohort in New York City. We integrated the molecular characterization of 800+ nasopharyngeal samples with clinical data from 104 participants. Transcriptomic data enabled the identification of respiratory pathogens in nasopharyngeal samples, the characterization of markers of immune response, the identification of signatures associated with symptom severity, individual viruses, and bacterial coinfections. Specific results include a rapid restoration of baseline conditions after infection, significant transcriptomic differences between symptomatic and asymptomatic infections, and qualitatively similar responses across different viruses. We created an interactive computational resource (Virome Data Explorer) to facilitate access to the data and visualization of analytical results.
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Affiliation(s)
- Marta Galanti
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Juan Angel Patiño-Galindo
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Ioan Filip
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Haruka Morita
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Angelica Galianese
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Mariam Youssef
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Devon Comito
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Chanel Ligon
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Benjamin Lane
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Nelsa Matienzo
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sadiat Ibrahim
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Eudosie Tagne
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Atinuke Shittu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Oliver Elliott
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Tomin Perea-Chamblee
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Sanjay Natesan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Daniel Scholes Rosenbloom
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
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Deshpande G, Beetch JE, Heller JG, Naqvi OH, Kuhn KG. Assessing the Influence of Climate Change and Environmental Factors on the Top Tick-Borne Diseases in the United States: A Systematic Review. Microorganisms 2023; 12:50. [PMID: 38257877 PMCID: PMC10821204 DOI: 10.3390/microorganisms12010050] [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: 11/28/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
In the United States (US), tick-borne diseases (TBDs) have more than doubled in the past fifteen years and are a major contributor to the overall burden of vector-borne diseases. The most common TBDs in the US-Lyme disease, rickettsioses (including Rocky Mountain spotted fever), and anaplasmosis-have gradually shifted in recent years, resulting in increased morbidity and mortality. In this systematic review, we examined climate change and other environmental factors that have influenced the epidemiology of these TBDs in the US while highlighting the opportunities for a One Health approach to mitigating their impact. We searched Medline Plus, PUBMED, and Google Scholar for studies focused on these three TBDs in the US from January 2018 to August 2023. Data selection and extraction were completed using Covidence, and the risk of bias was assessed with the ROBINS-I tool. The review included 84 papers covering multiple states across the US. We found that climate, seasonality and temporality, and land use are important environmental factors that impact the epidemiology and patterns of TBDs. The emerging trends, influenced by environmental factors, emphasize the need for region-specific research to aid in the prediction and prevention of TBDs.
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Affiliation(s)
| | | | | | | | - Katrin Gaardbo Kuhn
- Department of Biostatistics & Epidemiology, Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.D.); (J.E.B.); (J.G.H.); (O.H.N.)
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7
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Ko ER, Reller ME, Tillekeratne LG, Bodinayake CK, Miller C, Burke TW, Henao R, McClain MT, Suchindran S, Nicholson B, Blatt A, Petzold E, Tsalik EL, Nagahawatte A, Devasiri V, Rubach MP, Maro VP, Lwezaula BF, Kodikara-Arachichi W, Kurukulasooriya R, De Silva AD, Clark DV, Schully KL, Madut D, Dumler JS, Kato C, Galloway R, Crump JA, Ginsburg GS, Minogue TD, Woods CW. Host-response transcriptional biomarkers accurately discriminate bacterial and viral infections of global relevance. Sci Rep 2023; 13:22554. [PMID: 38110534 PMCID: PMC10728077 DOI: 10.1038/s41598-023-49734-6] [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: 12/27/2022] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Diagnostic limitations challenge management of clinically indistinguishable acute infectious illness globally. Gene expression classification models show great promise distinguishing causes of fever. We generated transcriptional data for a 294-participant (USA, Sri Lanka) discovery cohort with adjudicated viral or bacterial infections of diverse etiology or non-infectious disease mimics. We then derived and cross-validated gene expression classifiers including: 1) a single model to distinguish bacterial vs. viral (Global Fever-Bacterial/Viral [GF-B/V]) and 2) a two-model system to discriminate bacterial and viral in the context of noninfection (Global Fever-Bacterial/Viral/Non-infectious [GF-B/V/N]). We then translated to a multiplex RT-PCR assay and independent validation involved 101 participants (USA, Sri Lanka, Australia, Cambodia, Tanzania). The GF-B/V model discriminated bacterial from viral infection in the discovery cohort an area under the receiver operator curve (AUROC) of 0.93. Validation in an independent cohort demonstrated the GF-B/V model had an AUROC of 0.84 (95% CI 0.76-0.90) with overall accuracy of 81.6% (95% CI 72.7-88.5). Performance did not vary with age, demographics, or site. Host transcriptional response diagnostics distinguish bacterial and viral illness across global sites with diverse endemic pathogens.
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Affiliation(s)
- Emily R Ko
- Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Duke University Health System, Duke University School of Medicine, 3643 N. Roxboro St., Durham, NC, 27704, USA.
| | - Megan E Reller
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - L Gayani Tillekeratne
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Champica K Bodinayake
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Cameron Miller
- Clinical Research Unit, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Thomas W Burke
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ricardo Henao
- Department of Biostatistics and Informatics, Duke University, Durham, NC, USA
| | - Micah T McClain
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
| | - Sunil Suchindran
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Adam Blatt
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Elizabeth Petzold
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ephraim L Tsalik
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Danaher Diagnostics, Washington, DC, USA
| | - Ajith Nagahawatte
- Department of Microbiology, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Vasantha Devasiri
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Matthew P Rubach
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore, Singapore, Singapore
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
| | - Venance P Maro
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Bingileki F Lwezaula
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Maswenzi Regional Referral Hospital, Moshi, Tanzania
| | | | | | - Aruna D De Silva
- General Sir John Kotelawala Defence University, Colombo, Sri Lanka
| | - Danielle V Clark
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, MD, USA
| | - Kevin L Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, MD, USA
| | - Deng Madut
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - J Stephen Dumler
- Joint Departments of Pathology, School of Medicine, Uniformed Services University, Bethesda, MD, USA
| | - Cecilia Kato
- Centers for Disease Control and Prevention, National Center for Emerging Zoonotic Infectious Diseases, Atlanta, USA
| | - Renee Galloway
- Centers for Disease Control and Prevention, National Center for Emerging Zoonotic Infectious Diseases, Atlanta, USA
| | - John A Crump
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Geoffrey S Ginsburg
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- National Institute of Health, Bethesda, MD, USA
| | - Timothy D Minogue
- Diagnostic Systems Division, USAMRIID, Fort Detrick, Frederick, MD, USA
| | - Christopher W Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
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8
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Frishberg A, Milman N, Alpert A, Spitzer H, Asani B, Schiefelbein JB, Bakin E, Regev-Berman K, Priglinger SG, Schultze JL, Theis FJ, Shen-Orr SS. Reconstructing disease dynamics for mechanistic insights and clinical benefit. Nat Commun 2023; 14:6840. [PMID: 37891175 PMCID: PMC10611752 DOI: 10.1038/s41467-023-42354-8] [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: 01/18/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Diseases change over time, both phenotypically and in their underlying molecular processes. Though understanding disease progression dynamics is critical for diagnostics and treatment, capturing these dynamics is difficult due to their complexity and the high heterogeneity in disease development between individuals. We present TimeAx, an algorithm which builds a comparative framework for capturing disease dynamics using high-dimensional, short time-series data. We demonstrate the utility of TimeAx by studying disease progression dynamics for multiple diseases and data types. Notably, for urothelial bladder cancer tumorigenesis, we identify a stromal pro-invasion point on the disease progression axis, characterized by massive immune cell infiltration to the tumor microenvironment and increased mortality. Moreover, the continuous TimeAx model differentiates between early and late tumors within the same tumor subtype, uncovering molecular transitions and potential targetable pathways. Overall, we present a powerful approach for studying disease progression dynamics-providing improved molecular interpretability and clinical benefits for patient stratification and outcome prediction.
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Affiliation(s)
- Amit Frishberg
- Department of Immunology, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Institute of Computational Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- CytoReason, Tel-Aviv, Israel
| | - Neta Milman
- Department of Immunology, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ayelet Alpert
- Department of Immunology, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hannah Spitzer
- Institute of Computational Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- Institute for Stroke and Dementia Research (ISD), LMU University Hospital, LMU Munich, Germany
| | - Ben Asani
- Department of Ophthalmology, Ludwig-Maximilians-University, Munich, Germany
| | | | | | | | | | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, 85748, Garching, Germany
- Technical University of Munich, TUM School of Life Sciences Weihenstephan, 85354, Freising, Germany
| | - Shai S Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
- CytoReason, Tel-Aviv, Israel.
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9
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Hanson KE, Banerjee R, Doernberg SB, Evans SR, Komarow L, Satlin MJ, Schwager N, Simner PJ, Tillekeratne LG, Patel R. Priorities and Progress in Diagnostic Research by the Antibacterial Resistance Leadership Group. Clin Infect Dis 2023; 77:S314-S320. [PMID: 37843119 PMCID: PMC10578045 DOI: 10.1093/cid/ciad541] [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] [Indexed: 10/17/2023] Open
Abstract
The advancement of infectious disease diagnostics, along with studies devoted to infections caused by gram-negative and gram-positive bacteria, is a top scientific priority of the Antibacterial Resistance Leadership Group (ARLG). Diagnostic tests for infectious diseases are rapidly evolving and improving. However, the availability of rapid tests designed to determine antibacterial resistance or susceptibility directly in clinical specimens remains limited, especially for gram-negative organisms. Additionally, the clinical impact of many new tests, including an understanding of how best to use them to inform optimal antibiotic prescribing, remains to be defined. This review summarizes the recent work of the ARLG toward addressing these unmet needs in the diagnostics field and describes future directions for clinical research aimed at curbing the threat of antibiotic-resistant bacterial infections.
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Affiliation(s)
- Kimberly E Hanson
- Division of Infectious Diseases, Department of Medicine, University of Utah, Salt Lake City, Utah, USA
- Division of Clinical Microbiology, Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Ritu Banerjee
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sarah B Doernberg
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Scott R Evans
- Department of Biostatistics, George Washington University, Washington, DC, USA
| | - Lauren Komarow
- George Washington University Biostatistics Center, Rockville, Maryland, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Nyssa Schwager
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - L Gayani Tillekeratne
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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10
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Sofia de Olazarra A, Chen FE, Wang TH, Wang SX. Rapid, Point-of-Care Host-Based Gene Expression Diagnostics Using Giant Magnetoresistive Biosensors. ACS Sens 2023; 8:2780-2790. [PMID: 37368357 DOI: 10.1021/acssensors.3c00696] [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] [Indexed: 06/28/2023]
Abstract
Host-based gene expression analysis is a promising tool for a broad range of clinical applications, including rapid infectious disease diagnostics and real-time disease monitoring. However, the complex instrumentation requirements and slow turnaround-times associated with traditional gene expression analysis methods have hampered their widespread adoption at the point-of-care (POC). To overcome these challenges, we have developed an automated and portable platform that utilizes polymerase chain reaction (PCR) and giant magnetoresistive (GMR) biosensors to perform rapid multiplexed, targeted gene expression analysis at the POC. As proof-of-concept, we utilized our platform to amplify and measure the expression of four genes (HERC5, HERC6, IFI27, and IFIH1) that were previously shown to be upregulated in hosts infected with influenza viruses. The compact instrument conducted highly automated PCR amplification and GMR detection to measure the expression of the four genes in multiplex, then utilized Bluetooth communication to relay results to users on a smartphone application. To validate the platform, we tested 20 cDNA samples from symptomatic patients that had been previously diagnosed as either influenza-positive or influenza-negative using a RT-PCR virology panel. A non-parametric Mann-Whitney test revealed that day 0 (day of symptom onset) gene expression was significantly different between the two groups (p < 0.0001, n = 20). Hence, we preliminarily demonstrated that our platform could accurately discriminate between symptomatic influenza and non-influenza populations based on host gene expression in ∼30 min. This study not only establishes the potential clinical utility of our proposed assay and device for influenza diagnostics but it also paves the way for broadscale and decentralized implementation of host-based gene expression diagnostics at the POC.
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Affiliation(s)
- Ana Sofia de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94035, United States
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Shan X Wang
- Department of Electrical Engineering, Stanford University, Stanford, California 94035, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
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11
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Huo Y, Li C, Li Y, Li X, Xu P, Bao Z, Liu W. Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers. Brief Funct Genomics 2023:7036269. [PMID: 36787234 DOI: 10.1093/bfgp/elad006] [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: 10/03/2022] [Revised: 01/15/2023] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
As a dynamical system, complex disease always has a sudden state transition at the tipping point, which is the result of the long-term accumulation of abnormal regulations. This paper proposes a novel approach to detect the early-warning signals of influenza A (H3N2 and H1N1) outbreaks by dysregulated dynamic network biomarkers (dysregulated DNBs) for individuals. The results of cross-validation show that our approach can detect early-warning signals before the symptom appears successfully. Unlike the traditional DNBs, our dysregulated DNBs are anchored and very few, which is essential for disease early diagnosis in clinical practice. Moreover, the genes of dysregulated DNBs are significantly enriched in the influenza-related pathways. The source code of this paper can be freely downloaded from https://github.com/YanhaoHuo/dysregulated-DNBs.git.
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Affiliation(s)
- Yanhao Huo
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Chuchu Li
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Yujie Li
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Xianbin Li
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China.,School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, China
| | - Peng Xu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China.,School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, China
| | - Zhenshen Bao
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China.,School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, China
| | - Wenbin Liu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
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12
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Lim FY, Kim SY, Kulkarni KN, Blazevic RL, Kimball LE, Lea HG, Haack AJ, Gower MS, Stevens-Ayers T, Starita LM, Boeckh M, Schiffer JT, Hyrien O, Theberge AB, Waghmare A. Longitudinal home self-collection of capillary blood using homeRNA correlates interferon and innate viral defense pathways with SARS-CoV-2 viral clearance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.24.23284913. [PMID: 37034678 PMCID: PMC10081427 DOI: 10.1101/2023.01.24.23284913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Blood transcriptional profiling is a powerful tool to evaluate immune responses to infection; however, blood collection via traditional phlebotomy remains a barrier to precise characterization of the immune response in dynamic infections (e.g., respiratory viruses). Here we present an at-home self-collection methodology, homeRNA, to study the host transcriptional response during acute SARS-CoV-2 infections. This method uniquely enables high frequency measurement of the host immune kinetics in non-hospitalized adults during the acute and most dynamic stage of their infection. COVID-19+ and healthy participants self-collected blood every other day for two weeks with daily nasal swabs and symptom surveys to track viral load kinetics and symptom burden, respectively. While healthy uninfected participants showed remarkably stable immune kinetics with no significant dynamic genes, COVID-19+ participants, on the contrary, depicted a robust response with over 418 dynamic genes associated with interferon and innate viral defense pathways. When stratified by vaccination status, we detected distinct response signatures between unvaccinated and breakthrough (vaccinated) infection subgroups; unvaccinated individuals portrayed a response repertoire characterized by higher innate antiviral responses, interferon signaling, and cytotoxic lymphocyte responses while breakthrough infections portrayed lower levels of interferon signaling and enhanced early cell-mediated response. Leveraging cross-platform longitudinal sampling (nasal swabs and blood), we observed that IFI27, a key viral response gene, tracked closely with SARS-CoV-2 viral clearance in individual participants. Taken together, these results demonstrate that at-home sampling can capture key host antiviral responses and facilitate frequent longitudinal sampling to detect transient host immune kinetics during dynamic immune states.
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Affiliation(s)
- Fang Yun Lim
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
- Department of Chemistry, University of Washington; Seattle, Washington, U.S.A
| | - Soo-Young Kim
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
| | - Karisma N. Kulkarni
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
| | - Rachel L. Blazevic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
| | - Louise E. Kimball
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
| | - Hannah G. Lea
- Department of Chemistry, University of Washington; Seattle, Washington, U.S.A
| | - Amanda J. Haack
- Department of Chemistry, University of Washington; Seattle, Washington, U.S.A
| | - Maia. S. Gower
- Department of Chemistry, University of Washington; Seattle, Washington, U.S.A
| | - Terry Stevens-Ayers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
| | - Lea M. Starita
- Brotman Baty Institute, University of Washington, Seattle
- Department of Genome Sciences, University of Washington, Seattle
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
- Department of Medicine, University of Washington; Seattle, Washington, U.S.A
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
- Department of Medicine, University of Washington; Seattle, Washington, U.S.A
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
| | - Ashleigh B. Theberge
- Department of Chemistry, University of Washington; Seattle, Washington, U.S.A
- Department of Urology, University of Washington; Seattle, Washington, U.S.A
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, Washington, U.S.A
- Department of Pediatrics, University of Washington; Seattle, Washington, U.S.A
- Seattle Children’s Research Institute; Seattle, Washington, U.S.A
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13
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Tang J, Xu Q, Tang K, Ye X, Cao Z, Zou M, Zeng J, Guan X, Han J, Wang Y, Yang L, Lin Y, Jiang K, Chen X, Zhao Y, Tian D, Li C, Shen W, Du X. Susceptibility identification for seasonal influenza A/H3N2 based on baseline blood transcriptome. Front Immunol 2023; 13:1048774. [PMID: 36713410 PMCID: PMC9878565 DOI: 10.3389/fimmu.2022.1048774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction Influenza susceptibility difference is a widely existing trait that has great practical significance for the accurate prevention and control of influenza. Methods Here, we focused on the human susceptibility to the seasonal influenza A/H3N2 of healthy adults at baseline level. Whole blood expression data for influenza A/H3N2 susceptibility from GEO were collected firstly (30 symptomatic and 19 asymptomatic). Then to explore the differences at baseline, a suite of systems biology approaches - the differential expression analysis, co-expression network analysis, and immune cell frequencies analysis were utilized. Results We found the baseline condition, especially immune condition between symptomatic and asymptomatic, was different. Co-expression module that is positively related to asymptomatic is also related to immune cell type of naïve B cell. Function enrichment analysis showed significantly correlation with "B cell receptor signaling pathway", "immune response-activating cell surface receptor signaling pathway" and so on. Also, modules that are positively related to symptomatic are also correlated to immune cell type of neutrophils, with function enrichment analysis showing significantly correlations with "response to bacterium", "inflammatory response", "cAMP-dependent protein kinase complex" and so on. Responses of symptomatic and asymptomatic hosts after virus exposure show differences on resisting the virus, with more effective frontline defense for asymptomatic hosts. A prediction model was also built based on only baseline transcription information to differentiate symptomatic and asymptomatic population with accuracy of 0.79. Discussion The results not only improve our understanding of the immune system and influenza susceptibility, but also provide a new direction for precise and targeted prevention and therapy of influenza.
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Affiliation(s)
- Jing Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Qiumei Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China,Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Kang Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Ye
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zicheng Cao
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China,School of Public Health, Shantou University, Shantou, China
| | - Min Zou
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xinyan Guan
- Department of Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, China
| | - Jinglin Han
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Yihan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Lan Yang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China,School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yishan Lin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Kaiao Jiang
- Palos Verdes Peninsula High School, Rancho Palos Verdes, CA, United States
| | - Xiaoliang Chen
- Department of Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, China
| | - Yang Zhao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Dechao Tian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Chunwei Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Shen
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China,*Correspondence: Xiangjun Du, ; Wei Shen,
| | - Xiangjun Du
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China,*Correspondence: Xiangjun Du, ; Wei Shen,
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14
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Ko ER, Tsalik EL. A New Era in Host Response Biomarkers to Guide Precision Medicine for Infectious Diseases. J Pediatric Infect Dis Soc 2022; 11:477-479. [PMID: 35964237 DOI: 10.1093/jpids/piac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 07/21/2022] [Indexed: 11/14/2022]
Affiliation(s)
- Emily R Ko
- Section of Hospital Medicine, Division of General Internal Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Danaher Diagnostics, Washington DC, USA
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15
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Servellita V, Bouquet J, Rebman A, Yang T, Samayoa E, Miller S, Stone M, Lanteri M, Busch M, Tang P, Morshed M, Soloski MJ, Aucott J, Chiu CY. A diagnostic classifier for gene expression-based identification of early Lyme disease. COMMUNICATIONS MEDICINE 2022; 2:92. [PMID: 35879995 PMCID: PMC9306241 DOI: 10.1038/s43856-022-00127-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/17/2022] [Indexed: 11/26/2022] Open
Abstract
Background Lyme disease is a tick-borne illness that causes an estimated 476,000 infections annually in the United States. New diagnostic tests are urgently needed, as existing antibody-based assays lack sufficient sensitivity and specificity. Methods Here we perform transcriptome profiling by RNA sequencing (RNA-Seq), targeted RNA-Seq, and/or machine learning-based classification of 263 peripheral blood mononuclear cell samples from 218 subjects, including 94 early Lyme disease patients, 48 uninfected control subjects, and 57 patients with other infections (influenza, bacteremia, or tuberculosis). Differentially expressed genes among the 25,278 in the reference database are selected based on ≥1.5-fold change, ≤0.05 p value, and ≤0.001 false-discovery rate cutoffs. After gene selection using a k-nearest neighbor algorithm, the comparative performance of ten different classifier models is evaluated using machine learning. Results We identify a 31-gene Lyme disease classifier (LDC) panel that can discriminate between early Lyme patients and controls, with 23 genes (74.2%) that have previously been described in association with clinical investigations of Lyme disease patients or in vitro cell culture and rodent studies of Borrelia burgdorferi infection. Evaluation of the LDC using an independent test set of samples from 63 subjects yields an overall sensitivity of 90.0%, specificity of 100%, and accuracy of 95.2%. The LDC test is positive in 85.7% of seronegative patients and found to persist for ≥3 weeks in 9 of 12 (75%) patients. Conclusions These results highlight the potential clinical utility of a gene expression classifier for diagnosis of early Lyme disease, including in patients negative by conventional serologic testing. Lyme disease is a bacterial infection spread by ticks and there are nearly half a million cases a year in the United States. However, the disease is difficult to diagnose and existing laboratory tests have limited accuracy. Here, we develop a new genetic test, described as a Lyme disease classifier (LDC), for diagnosing early Lyme disease from blood samples by assessing the patient’s response to the infection. We find that the LDC can identify early Lyme disease patients (those presenting with symptoms within weeks of a tick bite) accurately, even before standard laboratory tests turn positive. In the future, the LDC may be clinically useful as a test for Lyme disease to diagnose patients earlier in the course of their illness, thus guiding more timely and effective treatment for the infection. Servellita et al. develop a machine learning-based classifier to diagnose Lyme disease using gene expression data. The classifier achieves high sensitivity for early infections, even prior to positivity on antibody testing.
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16
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Choy RKM, Bourgeois AL, Ockenhouse CF, Walker RI, Sheets RL, Flores J. Controlled Human Infection Models To Accelerate Vaccine Development. Clin Microbiol Rev 2022; 35:e0000821. [PMID: 35862754 PMCID: PMC9491212 DOI: 10.1128/cmr.00008-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The timelines for developing vaccines against infectious diseases are lengthy, and often vaccines that reach the stage of large phase 3 field trials fail to provide the desired level of protective efficacy. The application of controlled human challenge models of infection and disease at the appropriate stages of development could accelerate development of candidate vaccines and, in fact, has done so successfully in some limited cases. Human challenge models could potentially be used to gather critical information on pathogenesis, inform strain selection for vaccines, explore cross-protective immunity, identify immune correlates of protection and mechanisms of protection induced by infection or evoked by candidate vaccines, guide decisions on appropriate trial endpoints, and evaluate vaccine efficacy. We prepared this report to motivate fellow scientists to exploit the potential capacity of controlled human challenge experiments to advance vaccine development. In this review, we considered available challenge models for 17 infectious diseases in the context of the public health importance of each disease, the diversity and pathogenesis of the causative organisms, the vaccine candidates under development, and each model's capacity to evaluate them and identify correlates of protective immunity. Our broad assessment indicated that human challenge models have not yet reached their full potential to support the development of vaccines against infectious diseases. On the basis of our review, however, we believe that describing an ideal challenge model is possible, as is further developing existing and future challenge models.
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Affiliation(s)
- Robert K. M. Choy
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | - A. Louis Bourgeois
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | | | - Richard I. Walker
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | | | - Jorge Flores
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
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17
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Temple DS, Hegarty-Craver M, Furberg RD, Preble EA, Bergstrom E, Gardener Z, Dayananda P, Taylor L, Lemm NM, Papargyris L, McClain MT, Nicholson BP, Bowie A, Miggs M, Petzold E, Woods CW, Chiu C, Gilchrist KH. Wearable sensor-based detection of influenza in presymptomatic and asymptomatic individuals. J Infect Dis 2022; 227:864-872. [PMID: 35759279 PMCID: PMC9384446 DOI: 10.1093/infdis/jiac262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic highlighted the need for early detection of viral infections in symptomatic and asymptomatic individuals to allow for timely clinical management and public health interventions. METHODS Twenty healthy adults were challenged with an influenza A (H3N2) virus and prospectively monitored from 7 days before through 10 days after inoculation, using wearable electrocardiogram and physical activity sensors (Clinical Trial: NCT04204493; https://clinicaltrials.gov/ct2/show/NCT04204993). This framework allowed for responses to be accurately referenced to the infection event. For each participant, we trained a semi-supervised multivariable anomaly detection model on data acquired before inoculation and used it to classify the post-inoculation dataset. RESULTS Inoculation with this challenge virus was well-tolerated with an infection rate of 85%. With the model classification threshold set so that no alarms were recorded in the 170 healthy days recorded, the algorithm correctly identified 16 of 17 (94%) positive presymptomatic and asymptomatic individuals, on average 58 hours post inoculation and 23 hrs before the symptom onset. CONCLUSION The data processing and modeling methodology show promise for the early detection of respiratory illness. The detection algorithm is compatible with data collected from smartwatches using optical techniques but needs to be validated in large heterogeneous cohorts in normal living conditions.
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Affiliation(s)
| | | | | | | | - Emma Bergstrom
- Department of Infectious Disease, Imperial College London, London, SWT 2AZ, UK
| | - Zoe Gardener
- Department of Infectious Disease, Imperial College London, London, SWT 2AZ, UK
| | - Peter Dayananda
- Department of Infectious Disease, Imperial College London, London, SWT 2AZ, UK
| | - Lydia Taylor
- Department of Infectious Disease, Imperial College London, London, SWT 2AZ, UK
| | - Nana Marie Lemm
- Department of Infectious Disease, Imperial College London, London, SWT 2AZ, UK
| | - Lukas Papargyris
- Department of Infectious Disease, Imperial College London, London, SWT 2AZ, UK
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, 27710, USA
| | - Bradly P Nicholson
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, 27710, USA.,Institute for Medical Research, Durham, 27710, USA
| | - Aleah Bowie
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, 27710, USA
| | - Maria Miggs
- Institute for Medical Research, Durham, 27710, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, 27710, USA
| | - Christopher W Woods
- Institute for Medical Research, Durham, 27710, USA.,Hubert-Yeargan Center for Global Health, Duke University School of Medicine, Durham, 27710, USA
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, SWT 2AZ, UK
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18
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Stojanovic Z, Gonçalves-Carvalho F, Marín A, Abad Capa J, Domínguez J, Latorre I, Lacoma A, Prat-Aymerich C. Advances in diagnostic tools for respiratory tract infections. From tuberculosis to COVID19: changing paradigms? ERJ Open Res 2022; 8:00113-2022. [PMID: 36101788 PMCID: PMC9235056 DOI: 10.1183/23120541.00113-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/31/2022] [Indexed: 11/05/2022] Open
Abstract
Respiratory tract infections (RTI) are one of the commonest reasons for seeking healthcare, but are amongst the most challenging diseases in terms of clinical decision making. Proper and timely diagnosis is critical in order to optimize management and prevent further emergence of antimicrobial resistance by misuse, or overuse of antibiotics. Diagnostic tools for RTI include those involving syndromic and etiological diagnosis: from clinical and radiological features to laboratory methods targeting both pathogen detection and host biomarkers, as well as their combinations in terms of clinical algorithms. They also include tools for predicting severity and monitoring treatment response. Unprecedented milestones have been achieved in the context of the COVID-19 pandemic, involving the most recent applications of diagnostic technologies both at genotypic and phenotypic level, which have changed paradigms in infectious respiratory diseases in terms of why, how and where diagnostics are performed. The aim of this review is to discuss advances in diagnostic tools that impact clinical decision making, surveillance and follow-up of RTI and tuberculosis. If properly harnessed, recent advances in diagnostic technologies, including omics and digital transformation emerge as an unprecedented opportunity to tackle ongoing and future epidemics while handling antimicrobial resistance from a One Health perspective.
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19
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Ahmed U, Graf JF, Daytz A, Yaipen O, Mughrabi I, Jayaprakash N, Cotero V, Morton C, Deutschman CS, Zanos S, Puleo C. Ultrasound Neuromodulation of the Spleen Has Time-Dependent Anti-Inflammatory Effect in a Pneumonia Model. Front Immunol 2022; 13:892086. [PMID: 35784337 PMCID: PMC9244783 DOI: 10.3389/fimmu.2022.892086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/17/2022] [Indexed: 12/27/2022] Open
Abstract
Interfaces between the nervous and immune systems have been shown essential for the coordination and regulation of immune responses. Non-invasive ultrasound stimulation targeted to the spleen has recently been shown capable of activating one such interface, the splenic cholinergic anti-inflammatory pathway (CAP). Over the past decade, CAP and other neuroimmune pathways have been activated using implanted nerve stimulators and tested to prevent cytokine release and inflammation. However, CAP studies have typically been performed in models of severe, systemic (e.g., endotoxemia) or chronic inflammation (e.g., collagen-induced arthritis or DSS-induced colitis). Herein, we examined the effects of activation of the splenic CAP with ultrasound in a model of local bacterial infection by lung instillation of 105 CFU of Streptococcus pneumoniae. We demonstrate a time-dependent effect of CAP activation on the cytokine response assay during infection progression. CAP activation-induced cytokine suppression is absent at intermediate times post-infection (16 hours following inoculation), but present during the early (4 hours) and later phases (48 hours). These results indicate that cytokine inhibition associated with splenic CAP activation is not observed at all timepoints following bacterial infection and highlights the importance of further studying neuroimmune interfaces within the context of different immune system and inflammatory states.
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Affiliation(s)
- Umair Ahmed
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - John F. Graf
- General Electric Research, Niskayuna, NY, United States
| | - Anna Daytz
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Omar Yaipen
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Ibrahim Mughrabi
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Naveen Jayaprakash
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | | | | | - Clifford Scott Deutschman
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Stavros Zanos
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Chris Puleo
- General Electric Research, Niskayuna, NY, United States
- *Correspondence: Chris Puleo,
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20
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Gao R, Yan J, Li P, Chen L. Detecting the critical states during disease development based on temporal network flow entropy. Brief Bioinform 2022; 23:6587172. [PMID: 35580862 DOI: 10.1093/bib/bbac164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
Complex diseases progression can be generally divided into three states, which are normal state, predisease/critical state and disease state. The sudden deterioration of diseases can be viewed as a bifurcation or a critical transition. Therefore, hunting for the tipping point or critical state is of great importance to prevent the disease deterioration. However, it is still a challenging task to detect the critical states of complex diseases with high-dimensional data, especially based on an individual. In this study, we develop a new method based on network fluctuation of molecules, temporal network flow entropy (TNFE) or temporal differential network flow entropy, to detect the critical states of complex diseases on the basis of each individual. By applying this method to a simulated dataset and six real diseases, including respiratory viral infections and tumors with four time-course and two stage-course high-dimensional omics datasets, the critical states before deterioration were detected and their dynamic network biomarkers were identified successfully. The results on the simulated dataset indicate that the TNFE method is robust under different noise strengths, and is also superior to the existing methods on detecting the critical states. Moreover, the analysis on the real datasets demonstrated the effectiveness of TNFE for providing early-warning signals on various diseases. In addition, we also predicted disease deterioration risk and identified drug targets for cancers based on stage-wise data.
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Affiliation(s)
- Rong Gao
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang 471023, China
| | - Jinling Yan
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang 471023, China
| | - Peiluan Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang 471023, China
| | - Luonan Chen
- Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, Guangdong 519031, China.,International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo 113-0033, Japan
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21
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Sacco K, Castagnoli R, Vakkilainen S, Liu C, Delmonte OM, Oguz C, Kaplan IM, Alehashemi S, Burbelo PD, Bhuyan F, de Jesus AA, Dobbs K, Rosen LB, Cheng A, Shaw E, Vakkilainen MS, Pala F, Lack J, Zhang Y, Fink DL, Oikonomou V, Snow AL, Dalgard CL, Chen J, Sellers BA, Montealegre Sanchez GA, Barron K, Rey-Jurado E, Vial C, Poli MC, Licari A, Montagna D, Marseglia GL, Licciardi F, Ramenghi U, Discepolo V, Lo Vecchio A, Guarino A, Eisenstein EM, Imberti L, Sottini A, Biondi A, Mató S, Gerstbacher D, Truong M, Stack MA, Magliocco M, Bosticardo M, Kawai T, Danielson JJ, Hulett T, Askenazi M, Hu S, Cohen JI, Su HC, Kuhns DB, Lionakis MS, Snyder TM, Holland SM, Goldbach-Mansky R, Tsang JS, Notarangelo LD. Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19. Nat Med 2022; 28:1050-1062. [PMID: 35177862 PMCID: PMC9119950 DOI: 10.1038/s41591-022-01724-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022]
Abstract
Pediatric Coronavirus Disease 2019 (pCOVID-19) is rarely severe; however, a minority of children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) might develop multisystem inflammatory syndrome in children (MIS-C), with substantial morbidity. In this longitudinal multi-institutional study, we applied multi-omics (analysis of soluble biomarkers, proteomics, single-cell gene expression and immune repertoire analysis) to profile children with COVID-19 (n = 110) and MIS-C (n = 76), along with pediatric healthy controls (pHCs; n = 76). pCOVID-19 was characterized by robust type I interferon (IFN) responses, whereas prominent type II IFN-dependent and NF-κB-dependent signatures, matrisome activation and increased levels of circulating spike protein were detected in MIS-C, with no correlation with SARS-CoV-2 PCR status around the time of admission. Transient expansion of TRBV11-2 T cell clonotypes in MIS-C was associated with signatures of inflammation and T cell activation. The association of MIS-C with the combination of HLA A*02, B*35 and C*04 alleles suggests genetic susceptibility. MIS-C B cells showed higher mutation load than pCOVID-19 and pHC. These results identify distinct immunopathological signatures in pCOVID-19 and MIS-C that might help better define the pathophysiology of these disorders and guide therapy.
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Affiliation(s)
- Keith Sacco
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Riccardo Castagnoli
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Svetlana Vakkilainen
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Graduate Program in Biological Sciences, University of Maryland, College Park, MD, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cihan Oguz
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | | | - Sara Alehashemi
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Farzana Bhuyan
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adriana A de Jesus
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aristine Cheng
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Justin Lack
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Danielle L Fink
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vasileios Oikonomou
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jinguo Chen
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, USA
| | - Brian A Sellers
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, USA
| | - Gina A Montealegre Sanchez
- Intramural Clinical Management and Operation Branch (ICMOB), Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karyl Barron
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emma Rey-Jurado
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Maria Cecilia Poli
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Unidad de Inmunología y Reumatología, Hospital de niños Dr. Roberto del Río, Santiago, Chile
| | - Amelia Licari
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Daniela Montagna
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
- Laboratory of Immunology and Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gian Luigi Marseglia
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Francesco Licciardi
- Department of Pediatric and Public Health Sciences, Regina Margherita Children's Hospital, A.O.U. Città Della Salute E Della Scienza Di Torino, University of Turin, Turin, Italy
| | - Ugo Ramenghi
- Department of Pediatric and Public Health Sciences, Regina Margherita Children's Hospital, A.O.U. Città Della Salute E Della Scienza Di Torino, University of Turin, Turin, Italy
| | - Valentina Discepolo
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Andrea Lo Vecchio
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Alfredo Guarino
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Eli M Eisenstein
- Department of Pediatrics, Hadassah-Hebrew University Medical Center, Mount Scopus, Jerusalem, Israel
| | - Luisa Imberti
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN, University of Milano Bicocca, Fondazione MBBM, Ospedale San Gerardo, Monza, Italy
| | - Sayonara Mató
- Randall Children's Hospital at Legacy Emanuel, Portland, OR, USA
| | - Dana Gerstbacher
- Division of Pediatric Rheumatology, Stanford Children's Hospital, Stanford, CA, USA
| | - Meng Truong
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Stack
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tomoki Kawai
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey J Danielson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Hulett
- CDI Laboratories, Antygen Division, Baltimore, MD, USA
| | | | - Shaohui Hu
- CDI Laboratories, Antygen Division, Baltimore, MD, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Douglas B Kuhns
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raphaela Goldbach-Mansky
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIH Center for Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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22
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Holcomb ZE, Steinbrink JM, Zaas AK, Betancourt M, Tenor JL, Toffaletti DL, Alspaugh JA, Perfect JR, McClain MT. Transcriptional Profiles Elucidate Differential Host Responses to Infection with Cryptococcus neoformans and Cryptococcus gattii. J Fungi (Basel) 2022; 8:jof8050430. [PMID: 35628686 PMCID: PMC9143552 DOI: 10.3390/jof8050430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Many aspects of the host response to invasive cryptococcal infections remain poorly understood. In order to explore the pathobiology of infection with common clinical strains, we infected BALB/cJ mice with Cryptococcus neoformans, Cryptococcus gattii, or sham control, and assayed host transcriptomic responses in peripheral blood. Infection with C. neoformans resulted in markedly greater fungal burden in the CNS than C. gattii, as well as slightly higher fungal burden in the lungs. A total of 389 genes were significantly differentially expressed in response to C. neoformans infection, which mainly clustered into pathways driving immune function, including complement activation and TH2-skewed immune responses. C. neoformans infection demonstrated dramatic up-regulation of complement-driven genes and greater up-regulation of alternatively activated macrophage activity than seen with C gattii. A 27-gene classifier was built, capable of distinguishing cryptococcal infection from animals with bacterial infection due to Staphylococcus aureus with 94% sensitivity and 89% specificity. Top genes from the murine classifiers were also differentially expressed in human PBMCs following infection, suggesting cross-species relevance of these findings. The host response, as manifested in transcriptional profiles, informs our understanding of the pathophysiology of cryptococcal infection and demonstrates promise for contributing to development of novel diagnostic approaches.
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Affiliation(s)
- Zachary E. Holcomb
- Harvard Combined Dermatology Residency Program, Department of Dermatology, Massachusetts General Hospital, Boston, MA 02114, USA;
| | - Julie M. Steinbrink
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (A.K.Z.); (M.B.); (J.L.T.); (D.L.T.); (J.A.A.); (J.R.P.); (M.T.M.)
- Correspondence:
| | - Aimee K. Zaas
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (A.K.Z.); (M.B.); (J.L.T.); (D.L.T.); (J.A.A.); (J.R.P.); (M.T.M.)
| | - Marisol Betancourt
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (A.K.Z.); (M.B.); (J.L.T.); (D.L.T.); (J.A.A.); (J.R.P.); (M.T.M.)
| | - Jennifer L. Tenor
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (A.K.Z.); (M.B.); (J.L.T.); (D.L.T.); (J.A.A.); (J.R.P.); (M.T.M.)
| | - Dena L. Toffaletti
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (A.K.Z.); (M.B.); (J.L.T.); (D.L.T.); (J.A.A.); (J.R.P.); (M.T.M.)
| | - J. Andrew Alspaugh
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (A.K.Z.); (M.B.); (J.L.T.); (D.L.T.); (J.A.A.); (J.R.P.); (M.T.M.)
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John R. Perfect
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (A.K.Z.); (M.B.); (J.L.T.); (D.L.T.); (J.A.A.); (J.R.P.); (M.T.M.)
| | - Micah T. McClain
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (A.K.Z.); (M.B.); (J.L.T.); (D.L.T.); (J.A.A.); (J.R.P.); (M.T.M.)
- Infectious Diseases Section, Medical Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705, USA
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23
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Bajo-Morales J, Prieto-Prieto JC, Herrera LJ, Rojas I, Castillo-Secilla D. COVID-19 Biomarkers Recognition & Classification Using Intelligent Systems. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220328125029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background:
SARS-CoV-2 has paralyzed mankind due to its high transmissibility and its associated mortality, causing millions of infections and deaths worldwide. The search for gene expression biomarkers from the host transcriptional response to infection may help understand the underlying mechanisms by which the virus causes COVID-19. This research proposes a smart methodology integrating different RNA-Seq datasets from SARS-CoV-2, other respiratory diseases, and healthy patients.
Methods:
The proposed pipeline exploits the functionality of the ‘KnowSeq’ R/Bioc package, integrating different data sources and attaining a significantly larger gene expression dataset, thus endowing the results with higher statistical significance and robustness in comparison with previous studies in the literature. A detailed preprocessing step was carried out to homogenize the samples and build a clinical decision system for SARS-CoV-2. It uses machine learning techniques such as feature selection algorithm and supervised classification system. This clinical decision system uses the most differentially expressed genes among different diseases (including SARS-Cov-2) to develop a four-class classifier.
Results:
The multiclass classifier designed can discern SARS-CoV-2 samples, reaching an accuracy equal to 91.5%, a mean F1-Score equal to 88.5%, and a SARS-CoV-2 AUC equal to 94% by using only 15 genes as predictors. A biological interpretation of the gene signature extracted reveals relations with processes involved in viral responses.
Conclusion:
This work proposes a COVID-19 gene signature composed of 15 genes, selected after applying the feature selection ‘minimum Redundancy Maximum Relevance’ algorithm. The integration among several RNA-Seq datasets was a success, allowing for a considerable large number of samples and therefore providing greater statistical significance to the results than previous studies. Biological interpretation of the selected genes was also provided.
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Affiliation(s)
- Javier Bajo-Morales
- Department of Computer Architecture and Technology, University of Granada. C.I.T.I.C., Periodista Rafael Gómez Montero, 2, 18014, Granada, Spain
| | - Juan Carlos Prieto-Prieto
- Nuclear Medicine Department, IMIBIC, University Hospital Reina Sofia, Menéndez Pidal Avenue, 14004, Córdoba, Spain
| | - Luis Javier Herrera
- Department of Computer Architecture and Technology, University of Granada. C.I.T.I.C., Periodista Rafael Gómez Montero, 2, 18014, Granada, Spain
| | - Ignacio Rojas
- Department of Computer Architecture and Technology, University of Granada. C.I.T.I.C., Periodista Rafael Gómez Montero, 2, 18014, Granada, Spain
| | - Daniel Castillo-Secilla
- Department of Computer Architecture and Technology, University of Granada. C.I.T.I.C., Periodista Rafael Gómez Montero, 2, 18014, Granada, Spain
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24
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Zan A, Xie ZR, Hsu YC, Chen YH, Lin TH, Chang YS, Chang KY. DeepFlu: a deep learning approach for forecasting symptomatic influenza A infection based on pre-exposure gene expression. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 213:106495. [PMID: 34798406 DOI: 10.1016/j.cmpb.2021.106495] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND OBJECTIVE Not everyone gets sick after an exposure to influenza A viruses (IAV). Although KLRD1 has been identified as a potential biomarker for influenza susceptibility, it remains unclear whether forecasting symptomatic flu infection based on pre-exposure host gene expression might be possible. METHOD To examine this hypothesis, we developed DeepFlu using the state-of-the-art deep learning approach on the human gene expression data infected with IAV subtype H1N1 or H3N2 viruses to forecast who would catch the flu prior to an exposure to IAV. RESULTS The results indicated that such forecast is possible and, in other words, gene expression could reflect the strength of host immunity. In the leave-one-person-out cross-validation, DeepFlu based on deep neural network outperformed the models using convolutional neural network, random forest, or support vector machine, achieving 70.0% accuracy, 0.787 AUROC, and 0.758 AUPR for H1N1 and 73.8% accuracy, 0.847 AUROC, and 0.901 AUPR for H3N2. In the external validation, DeepFlu also reached 71.4% accuracy, 0.700 AUROC, and 0.723 AUPR for H1N1 and 73.5% accuracy, 0.732 AUROC, and 0.749 AUPR for H3N2, surpassing the KLRD1 biomarker. In addition, DeepFlu which was trained only by pre-exposure data worked the best than by other time spans and mixed training data of H1N1 and H3N2 did not necessarily enhance prediction. DeepFlu is available at https://github.com/ntou-compbio/DeepFlu. CONCLUSIONS DeepFlu is a prognostic tool that can moderately recognize individuals susceptible to the flu and may help prevent the spread of IAV.
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Affiliation(s)
- Anna Zan
- Computational Biology Laboratory, Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung Taiwan, ROC
| | - Zhong-Ru Xie
- Computational Drug Discovery Laboratory, School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens GA, USA
| | - Yi-Chen Hsu
- Computational Biology Laboratory, Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung Taiwan, ROC
| | - Yu-Hao Chen
- Computational Biology Laboratory, Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung Taiwan, ROC
| | - Tsung-Hsien Lin
- Computational Biology Laboratory, Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung Taiwan, ROC
| | - Yong-Shan Chang
- Computational Biology Laboratory, Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung Taiwan, ROC
| | - Kuan Y Chang
- Computational Biology Laboratory, Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung Taiwan, ROC.
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Jaffe IS, Jaehne AK, Quackenbush E, Ko ER, Rivers EP, McClain MT, Ginsburg GS, Woods CW, Tsalik EL. Comparing the Diagnostic Accuracy of Clinician Judgment to a Novel Host Response Diagnostic for Acute Respiratory Illness. Open Forum Infect Dis 2021; 8:ofab564. [PMID: 34888402 DOI: 10.1093/ofid/ofab564] [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: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 11/12/2022] Open
Abstract
Background Difficulty discriminating bacterial from viral infections drives antibacterial misuse. Host gene expression tests discriminate bacterial and viral etiologies, but their clinical utility has not been evaluated. Methods Host gene expression and procalcitonin levels were measured in 582 emergency department participants with suspected infection. We also recorded clinician diagnosis and clinician-recommended treatment. These 4 diagnostic strategies were compared with clinical adjudication as the reference. To estimate the clinical impact of host gene expression, we calculated the change in overall Net Benefit (∆NB; the difference in Net Benefit comparing 1 diagnostic strategy with a reference) across a range of prevalence estimates while factoring in the clinical significance of false-positive and -negative errors. Results Gene expression correctly classified bacterial, viral, or noninfectious illness in 74.1% of subjects, similar to the other strategies. Clinical diagnosis and clinician-recommended treatment revealed a bias toward overdiagnosis of bacterial infection resulting in high sensitivity (92.6% and 94.5%, respectively) but poor specificity (67.2% and 58.8%, respectively), resulting in a 33.3% rate of inappropriate antibacterial use. Gene expression offered a more balanced sensitivity (79.0%) and specificity (80.7%), which corresponded to a statistically significant improvement in average weighted accuracy (79.9% vs 71.5% for procalcitonin and 76.3% for clinician-recommended treatment; P<.0001 for both). Consequently, host gene expression had greater Net Benefit in diagnosing bacterial infection than clinician-recommended treatment (∆NB=6.4%) and procalcitonin (∆NB=17.4%). Conclusions Host gene expression-based tests to distinguish bacterial and viral infection can facilitate appropriate treatment, improving patient outcomes and mitigating the antibacterial resistance crisis.
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Affiliation(s)
- Ian S Jaffe
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Anja K Jaehne
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, Michigan, USA
| | - Eugenia Quackenbush
- Department of Emergency Medicine, University of North Carolina Medical Center, Chapel Hill, North Carolina, USA
| | - Emily R Ko
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Emanuel P Rivers
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, Michigan, USA
| | - Micah T McClain
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medical Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher W Woods
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medical Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
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Differential Analysis and Putative Roles of Genes, Cytokines and Apoptotic Proteins in Blood Samples of Patients with Respiratory Viral Infections: A Single Center Study. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Insights into the molecular pathogenesis of respiratory viral infections were investigated using serum and peripheral blood from patients with clinical syndromes. Signatures of expression of cytokines, genes and apoptotic proteins that discriminate symptomatic individuals from healthy individuals were determined among 21 patients. In symptomatic patients, significant upregulation of IL-1β, IL-2, IL-4, IL-6, IL-8, IL-12, IL-15, TNF-a and IFN-g (P<0.05) was noted, while IL-10 was significantly downregulated (P<0.05). This is accompanied by either up or down-regulation of various pro-apoptotic and anti-apoptotic markers, suggesting a protective role of immune responses against viral infection and the capacity of viruses to subvert host cell apoptosis. Gene expression analysis for both T and B cells were categorized according to their functional status of activation, proliferation, and differentiation. Of note, genes SH2D1A and TCL1A were upregulated only in rhinovirus samples, while PSMB7, CD4, CD8A, HLA-DMA, HLA-DRA and CD69 were upregulated in samples of Flu A and RSV but were not significant in samples of rhinovirus as compared to healthy individuals. These results demonstrated Flu A and RSV elicit different alterations in human peripheral blood gene expression as compared to rhinovirus. Overall, despite the small number of study subjects, the current study for the first time has recognized signature genes, cytokines and proteins that are used by some respiratory viruses that may serve as candidates for rapid diagnosis as well as targets for therapeutic interventions.
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27
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Tsalik EL, Fiorino C, Aqeel A, Liu Y, Henao R, Ko ER, Burke TW, Reller ME, Bodinayake CK, Nagahawatte A, Arachchi WK, Devasiri V, Kurukulasooriya R, McClain MT, Woods CW, Ginsburg GS, Tillekeratne LG, Schughart K. The Host Response to Viral Infections Reveals Common and Virus-Specific Signatures in the Peripheral Blood. Front Immunol 2021; 12:741837. [PMID: 34777354 PMCID: PMC8578928 DOI: 10.3389/fimmu.2021.741837] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Viruses cause a wide spectrum of clinical disease, the majority being acute respiratory infections (ARI). In most cases, ARI symptoms are similar for different viruses although severity can be variable. The objective of this study was to understand the shared and unique elements of the host transcriptional response to different viral pathogens. We identified 162 subjects in the US and Sri Lanka with infections due to influenza, enterovirus/rhinovirus, human metapneumovirus, dengue virus, cytomegalovirus, Epstein Barr Virus, or adenovirus. Our dataset allowed us to identify common pathways at the molecular level as well as virus-specific differences in the host immune response. Conserved elements of the host response to these viral infections highlighted the importance of interferon pathway activation. However, the magnitude of the responses varied between pathogens. We also identified virus-specific responses to influenza, enterovirus/rhinovirus, and dengue infections. Influenza-specific differentially expressed genes (DEG) revealed up-regulation of pathways related to viral defense and down-regulation of pathways related to T cell and neutrophil responses. Functional analysis of entero/rhinovirus-specific DEGs revealed up-regulation of pathways for neutrophil activation, negative regulation of immune response, and p38MAPK cascade and down-regulation of virus defenses and complement activation. Functional analysis of dengue-specific up-regulated DEGs showed enrichment of pathways for DNA replication and cell division whereas down-regulated DEGs were mainly associated with erythrocyte and myeloid cell homeostasis, reactive oxygen and peroxide metabolic processes. In conclusion, our study will contribute to a better understanding of molecular mechanisms to viral infections in humans and the identification of biomarkers to distinguish different types of viral infections.
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Affiliation(s)
- Ephraim L. Tsalik
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Emergency Department Service, Durham Veterans Affairs Health Care System, Durham, NC, United States
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Cassandra Fiorino
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Ammara Aqeel
- Duke Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Yiling Liu
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Ricardo Henao
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, United States
| | - Emily R. Ko
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Department of Medicine, Duke Regional Hospital, Durham, NC, United States
| | - Thomas W. Burke
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Megan E. Reller
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | | | | | | | | | | | - Micah T. McClain
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, United States
- Medical Service, Durham Veterans Affairs Health Care System, Durham, NC, United States
| | - Christopher W. Woods
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, United States
- Medical Service, Durham Veterans Affairs Health Care System, Durham, NC, United States
| | - Geoffrey S. Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - L. Gayani Tillekeratne
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, United States
- Medical Service, Durham Veterans Affairs Health Care System, Durham, NC, United States
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
- University of Veterinary Medicine Hannover, Hannover, Germany
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
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Tsalik EL, Henao R, Montgomery JL, Nawrocki JW, Aydin M, Lydon EC, Ko ER, Petzold E, Nicholson BP, Cairns CB, Glickman SW, Quackenbush E, Kingsmore SF, Jaehne AK, Rivers EP, Langley RJ, Fowler VG, McClain MT, Crisp RJ, Ginsburg GS, Burke TW, Hemmert AC, Woods CW. Discriminating Bacterial and Viral Infection Using a Rapid Host Gene Expression Test. Crit Care Med 2021; 49:1651-1663. [PMID: 33938716 PMCID: PMC8448917 DOI: 10.1097/ccm.0000000000005085] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Host gene expression signatures discriminate bacterial and viral infection but have not been translated to a clinical test platform. This study enrolled an independent cohort of patients to describe and validate a first-in-class host response bacterial/viral test. DESIGN Subjects were recruited from 2006 to 2016. Enrollment blood samples were collected in an RNA preservative and banked for later testing. The reference standard was an expert panel clinical adjudication, which was blinded to gene expression and procalcitonin results. SETTING Four U.S. emergency departments. PATIENTS Six-hundred twenty-three subjects with acute respiratory illness or suspected sepsis. INTERVENTIONS Forty-five-transcript signature measured on the BioFire FilmArray System (BioFire Diagnostics, Salt Lake City, UT) in ~45 minutes. MEASUREMENTS AND MAIN RESULTS Host response bacterial/viral test performance characteristics were evaluated in 623 participants (mean age 46 yr; 45% male) with bacterial infection, viral infection, coinfection, or noninfectious illness. Performance of the host response bacterial/viral test was compared with procalcitonin. The test provided independent probabilities of bacterial and viral infection in ~45 minutes. In the 213-subject training cohort, the host response bacterial/viral test had an area under the curve for bacterial infection of 0.90 (95% CI, 0.84-0.94) and 0.92 (95% CI, 0.87-0.95) for viral infection. Independent validation in 209 subjects revealed similar performance with an area under the curve of 0.85 (95% CI, 0.78-0.90) for bacterial infection and 0.91 (95% CI, 0.85-0.94) for viral infection. The test had 80.1% (95% CI, 73.7-85.4%) average weighted accuracy for bacterial infection and 86.8% (95% CI, 81.8-90.8%) for viral infection in this validation cohort. This was significantly better than 68.7% (95% CI, 62.4-75.4%) observed for procalcitonin (p < 0.001). An additional cohort of 201 subjects with indeterminate phenotypes (coinfection or microbiology-negative infections) revealed similar performance. CONCLUSIONS The host response bacterial/viral measured using the BioFire System rapidly and accurately discriminated bacterial and viral infection better than procalcitonin, which can help support more appropriate antibiotic use.
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Affiliation(s)
- Ephraim L. Tsalik
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Informatics, Duke University, Durham, NC, USA
- Duke Clinical Research Institute, Durham, NC, USA
| | | | | | - Mert Aydin
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Emily C. Lydon
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Emily R. Ko
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Regional Hospital, Durham, NC, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Charles B. Cairns
- University of North Carolina Medical Center, Chapel Hill, NC, USA
- Drexel University, Philadelphia, PA, USA
| | - Seth W. Glickman
- University of North Carolina Medical Center, Chapel Hill, NC, USA
| | | | | | | | | | | | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Durham, NC, USA
| | - Micah T. McClain
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Geoffrey S. Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Christopher W. Woods
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
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Davis S, Milechin L, Patel T, Hernandez M, Ciccarelli G, Samsi S, Hensley L, Goff A, Trefry J, Johnston S, Purcell B, Cabrera C, Fleischman J, Reuther A, Claypool K, Rossi F, Honko A, Pratt W, Swiston A. Detecting Pathogen Exposure During the Non-symptomatic Incubation Period Using Physiological Data: Proof of Concept in Non-human Primates. Front Physiol 2021; 12:691074. [PMID: 34552498 PMCID: PMC8451540 DOI: 10.3389/fphys.2021.691074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022] Open
Abstract
Background and Objectives: Early warning of bacterial and viral infection, prior to the development of overt clinical symptoms, allows not only for improved patient care and outcomes but also enables faster implementation of public health measures (patient isolation and contact tracing). Our primary objectives in this effort are 3-fold. First, we seek to determine the upper limits of early warning detection through physiological measurements. Second, we investigate whether the detected physiological response is specific to the pathogen. Third, we explore the feasibility of extending early warning detection with wearable devices. Research Methods: For the first objective, we developed a supervised random forest algorithm to detect pathogen exposure in the asymptomatic period prior to overt symptoms (fever). We used high-resolution physiological telemetry data (aortic blood pressure, intrathoracic pressure, electrocardiograms, and core temperature) from non-human primate animal models exposed to two viral pathogens: Ebola and Marburg (N = 20). Second, to determine reusability across different pathogens, we evaluated our algorithm against three independent physiological datasets from non-human primate models (N = 13) exposed to three different pathogens: Lassa and Nipah viruses and Y. pestis. For the third objective, we evaluated performance degradation when the algorithm was restricted to features derived from electrocardiogram (ECG) waveforms to emulate data from a non-invasive wearable device. Results: First, our cross-validated random forest classifier provides a mean early warning of 51 ± 12 h, with an area under the receiver-operating characteristic curve (AUC) of 0.93 ± 0.01. Second, our algorithm achieved comparable performance when applied to datasets from different pathogen exposures – a mean early warning of 51 ± 14 h and AUC of 0.95 ± 0.01. Last, with a degraded feature set derived solely from ECG, we observed minimal degradation – a mean early warning of 46 ± 14 h and AUC of 0.91 ± 0.001. Conclusion: Under controlled experimental conditions, physiological measurements can provide over 2 days of early warning with high AUC. Deviations in physiological signals following exposure to a pathogen are due to the underlying host’s immunological response and are not specific to the pathogen. Pre-symptomatic detection is strong even when features are limited to ECG-derivatives, suggesting that this approach may translate to non-invasive wearable devices.
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Affiliation(s)
- Shakti Davis
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Lauren Milechin
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Tejash Patel
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Mark Hernandez
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Greg Ciccarelli
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Siddharth Samsi
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Lisa Hensley
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, United States
| | - Arthur Goff
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, United States
| | - John Trefry
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, United States
| | - Sara Johnston
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, United States
| | - Bret Purcell
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, United States
| | - Catherine Cabrera
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Jack Fleischman
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Albert Reuther
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Kajal Claypool
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
| | - Franco Rossi
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, United States
| | - Anna Honko
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, United States
| | - William Pratt
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, United States
| | - Albert Swiston
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, United States
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30
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Grzesiak E, Bent B, McClain MT, Woods CW, Tsalik EL, Nicholson BP, Veldman T, Burke TW, Gardener Z, Bergstrom E, Turner RB, Chiu C, Doraiswamy PM, Hero A, Henao R, Ginsburg GS, Dunn J. Assessment of the Feasibility of Using Noninvasive Wearable Biometric Monitoring Sensors to Detect Influenza and the Common Cold Before Symptom Onset. JAMA Netw Open 2021; 4:e2128534. [PMID: 34586364 PMCID: PMC8482058 DOI: 10.1001/jamanetworkopen.2021.28534] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
IMPORTANCE Currently, there are no presymptomatic screening methods to identify individuals infected with a respiratory virus to prevent disease spread and to predict their trajectory for resource allocation. OBJECTIVE To evaluate the feasibility of using noninvasive, wrist-worn wearable biometric monitoring sensors to detect presymptomatic viral infection after exposure and predict infection severity in patients exposed to H1N1 influenza or human rhinovirus. DESIGN, SETTING, AND PARTICIPANTS The cohort H1N1 viral challenge study was conducted during 2018; data were collected from September 11, 2017, to May 4, 2018. The cohort rhinovirus challenge study was conducted during 2015; data were collected from September 14 to 21, 2015. A total of 39 adult participants were recruited for the H1N1 challenge study, and 24 adult participants were recruited for the rhinovirus challenge study. Exclusion criteria for both challenges included chronic respiratory illness and high levels of serum antibodies. Participants in the H1N1 challenge study were isolated in a clinic for a minimum of 8 days after inoculation. The rhinovirus challenge took place on a college campus, and participants were not isolated. EXPOSURES Participants in the H1N1 challenge study were inoculated via intranasal drops of diluted influenza A/California/03/09 (H1N1) virus with a mean count of 106 using the median tissue culture infectious dose (TCID50) assay. Participants in the rhinovirus challenge study were inoculated via intranasal drops of diluted human rhinovirus strain type 16 with a count of 100 using the TCID50 assay. MAIN OUTCOMES AND MEASURES The primary outcome measures included cross-validated performance metrics of random forest models to screen for presymptomatic infection and predict infection severity, including accuracy, precision, sensitivity, specificity, F1 score, and area under the receiver operating characteristic curve (AUC). RESULTS A total of 31 participants with H1N1 (24 men [77.4%]; mean [SD] age, 34.7 [12.3] years) and 18 participants with rhinovirus (11 men [61.1%]; mean [SD] age, 21.7 [3.1] years) were included in the analysis after data preprocessing. Separate H1N1 and rhinovirus detection models, using only data on wearble devices as input, were able to distinguish between infection and noninfection with accuracies of up to 92% for H1N1 (90% precision, 90% sensitivity, 93% specificity, and 90% F1 score, 0.85 [95% CI, 0.70-1.00] AUC) and 88% for rhinovirus (100% precision, 78% sensitivity, 100% specificity, 88% F1 score, and 0.96 [95% CI, 0.85-1.00] AUC). The infection severity prediction model was able to distinguish between mild and moderate infection 24 hours prior to symptom onset with an accuracy of 90% for H1N1 (88% precision, 88% sensitivity, 92% specificity, 88% F1 score, and 0.88 [95% CI, 0.72-1.00] AUC) and 89% for rhinovirus (100% precision, 75% sensitivity, 100% specificity, 86% F1 score, and 0.95 [95% CI, 0.79-1.00] AUC). CONCLUSIONS AND RELEVANCE This cohort study suggests that the use of a noninvasive, wrist-worn wearable device to predict an individual's response to viral exposure prior to symptoms is feasible. Harnessing this technology would support early interventions to limit presymptomatic spread of viral respiratory infections, which is timely in the era of COVID-19.
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Affiliation(s)
- Emilia Grzesiak
- Biomedical Engineering Department, Duke University, Durham, North Carolina
| | - Brinnae Bent
- Biomedical Engineering Department, Duke University, Durham, North Carolina
| | - Micah T. McClain
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina
| | - Christopher W. Woods
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina
- Durham Veterans Affairs Medical Center, Durham, North Carolina
- Department of Medicine, Duke Global Health Institute, Durham, North Carolina
| | - Ephraim L. Tsalik
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina
- Durham Veterans Affairs Medical Center, Durham, North Carolina
| | | | - Timothy Veldman
- Department of Medicine, Duke Global Health Institute, Durham, North Carolina
| | - Thomas W. Burke
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina
| | - Zoe Gardener
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Emma Bergstrom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ronald B. Turner
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - P. Murali Doraiswamy
- Department of Psychiatry, Duke University School of Medicine, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Alfred Hero
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor
| | - Ricardo Henao
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina
| | - Geoffrey S. Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina
| | - Jessilyn Dunn
- Biomedical Engineering Department, Duke University, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
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Steinbrink JM, Myers RA, Hua K, Johnson MD, Seidelman JL, Tsalik EL, Henao R, Ginsburg GS, Woods CW, Alexander BD, McClain MT. The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches. Genome Med 2021; 13:108. [PMID: 34225776 PMCID: PMC8259367 DOI: 10.1186/s13073-021-00924-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Candidemia is one of the most common nosocomial bloodstream infections in the United States, causing significant morbidity and mortality in hospitalized patients, but the breadth of the host response to Candida infections in human patients remains poorly defined. METHODS In order to better define the host response to Candida infection at the transcriptional level, we performed RNA sequencing on serial peripheral blood samples from 48 hospitalized patients with blood cultures positive for Candida species and compared them to patients with other acute viral, bacterial, and non-infectious illnesses. Regularized multinomial regression was utilized to develop pathogen class-specific gene expression classifiers. RESULTS Candidemia triggers a unique, robust, and conserved transcriptomic response in human hosts with 1641 genes differentially upregulated compared to healthy controls. Many of these genes corresponded to components of the immune response to fungal infection, heavily weighted toward neutrophil activation, heme biosynthesis, and T cell signaling. We developed pathogen class-specific classifiers from these unique signals capable of identifying and differentiating candidemia, viral, or bacterial infection across a variety of hosts with a high degree of accuracy (auROC 0.98 for candidemia, 0.99 for viral and bacterial infection). This classifier was validated on two separate human cohorts (auROC 0.88 for viral infection and 0.87 for bacterial infection in one cohort; auROC 0.97 in another cohort) and an in vitro model (auROC 0.94 for fungal infection, 0.96 for bacterial, and 0.90 for viral infection). CONCLUSIONS Transcriptional analysis of circulating leukocytes in patients with acute Candida infections defines novel aspects of the breadth of the human immune response during candidemia and suggests promising diagnostic approaches for simultaneously differentiating multiple types of clinical illnesses in at-risk, acutely ill patients.
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Affiliation(s)
- Julie M Steinbrink
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA.
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA.
| | - Rachel A Myers
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Kaiyuan Hua
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Melissa D Johnson
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Jessica L Seidelman
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Ephraim L Tsalik
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Christopher W Woods
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Division of Infectious Diseases, Durham Veterans Affairs Health Care System, Durham, NC, USA
| | - Barbara D Alexander
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Micah T McClain
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Division of Infectious Diseases, Durham Veterans Affairs Health Care System, Durham, NC, USA
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Cortese M, Sherman AC, Rouphael NG, Pulendran B. Systems Biological Analysis of Immune Response to Influenza Vaccination. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038596. [PMID: 32152245 DOI: 10.1101/cshperspect.a038596] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The last decade has witnessed tremendous progress in immunology and vaccinology, owing to several scientific and technological breakthroughs. Systems vaccinology is a field that has emerged at the forefront of vaccine research and development and provides a unique way to probe immune responses to vaccination in humans. The goals of systems vaccinology are to use systems-based approaches to define signatures that can be used to predict vaccine immunogenicity and efficacy and to delineate the molecular mechanisms driving protective immunity. The application of systems biological approaches in influenza vaccination studies has enabled the discovery of early signatures that predict immunogenicity to vaccination and yielded novel mechanistic insights about vaccine-induced immunity. Here we review the contributions of systems vaccinology to influenza vaccine development and critically examine the potential of systems vaccinology toward enabling the development of a universal influenza vaccine that provides robust and durable immunity against diverse influenza viruses.
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Affiliation(s)
- Mario Cortese
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Amy C Sherman
- Hope Clinic of the Emory Vaccine Center, Decatur, Georgia 30030, USA
| | - Nadine G Rouphael
- Hope Clinic of the Emory Vaccine Center, Decatur, Georgia 30030, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California 94305, USA.,Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA.,Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA
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Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping. Mod Pathol 2021; 34:1093-1103. [PMID: 33536572 PMCID: PMC7856856 DOI: 10.1038/s41379-020-00730-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 02/04/2023]
Abstract
There is an urgent and unprecedented need for sensitive and high-throughput molecular diagnostic tests to combat the SARS-CoV-2 pandemic. Here we present a generalized version of the RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) assay, called "capture RASL-seq" (cRASL-seq), which enables highly sensitive (down to ~1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ~10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid purification or reverse transcription, steps that have introduced supply bottlenecks into standard assay workflows. Our simplified protocol additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new technology with the potential to help mitigate the current pandemic and prevent similar public health crises.
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Liu C, Martins AJ, Lau WW, Rachmaninoff N, Chen J, Imberti L, Mostaghimi D, Fink DL, Burbelo PD, Dobbs K, Delmonte OM, Bansal N, Failla L, Sottini A, Quiros-Roldan E, Han KL, Sellers BA, Cheung F, Sparks R, Chun TW, Moir S, Lionakis MS, Rossi C, Su HC, Kuhns DB, Cohen JI, Notarangelo LD, Tsang JS. Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19. Cell 2021; 184:1836-1857.e22. [PMID: 33713619 PMCID: PMC7874909 DOI: 10.1016/j.cell.2021.02.018] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/16/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023]
Abstract
COVID-19 exhibits extensive patient-to-patient heterogeneity. To link immune response variation to disease severity and outcome over time, we longitudinally assessed circulating proteins as well as 188 surface protein markers, transcriptome, and T cell receptor sequence simultaneously in single peripheral immune cells from COVID-19 patients. Conditional-independence network analysis revealed primary correlates of disease severity, including gene expression signatures of apoptosis in plasmacytoid dendritic cells and attenuated inflammation but increased fatty acid metabolism in CD56dimCD16hi NK cells linked positively to circulating interleukin (IL)-15. CD8+ T cell activation was apparent without signs of exhaustion. Although cellular inflammation was depressed in severe patients early after hospitalization, it became elevated by days 17-23 post symptom onset, suggestive of a late wave of inflammatory responses. Furthermore, circulating protein trajectories at this time were divergent between and predictive of recovery versus fatal outcomes. Our findings stress the importance of timing in the analysis, clinical monitoring, and therapeutic intervention of COVID-19.
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Affiliation(s)
- Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Graduate Program in Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - William W Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Office of Intramural Research, CIT, NIH, Bethesda, MD 20892, USA
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Graduate Program in Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia 25123, Italy
| | - Darius Mostaghimi
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Danielle L Fink
- Neutrophil Monitoring Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 20701, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD 20892, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Laura Failla
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alessandra Sottini
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia 25123, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili di Brescia, Brescia 25123, Italy
| | - Kyu Lee Han
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Rachel Sparks
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Susan Moir
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Camillo Rossi
- ASST Spedali Civili di Brescia, Brescia 25123, Italy
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 20701, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA.
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Dysregulated transcriptional responses to SARS-CoV-2 in the periphery. Nat Commun 2021; 12:1079. [PMID: 33597532 PMCID: PMC7889643 DOI: 10.1038/s41467-021-21289-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/15/2021] [Indexed: 01/31/2023] Open
Abstract
SARS-CoV-2 infection has been shown to trigger a wide spectrum of immune responses and clinical manifestations in human hosts. Here, we sought to elucidate novel aspects of the host response to SARS-CoV-2 infection through RNA sequencing of peripheral blood samples from 46 subjects with COVID-19 and directly comparing them to subjects with seasonal coronavirus, influenza, bacterial pneumonia, and healthy controls. Early SARS-CoV-2 infection triggers a powerful transcriptomic response in peripheral blood with conserved components that are heavily interferon-driven but also marked by indicators of early B-cell activation and antibody production. Interferon responses during SARS-CoV-2 infection demonstrate unique patterns of dysregulated expression compared to other infectious and healthy states. Heterogeneous activation of coagulation and fibrinolytic pathways are present in early COVID-19, as are IL1 and JAK/STAT signaling pathways, which persist into late disease. Classifiers based on differentially expressed genes accurately distinguished SARS-CoV-2 infection from other acute illnesses (auROC 0.95 [95% CI 0.92-0.98]). The transcriptome in peripheral blood reveals both diverse and conserved components of the immune response in COVID-19 and provides for potential biomarker-based approaches to diagnosis.
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Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CSS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY. A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. SCIENCE ADVANCES 2021; 7:eabe5984. [PMID: 33536218 PMCID: PMC7857687 DOI: 10.1126/sciadv.abe5984] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/15/2020] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning-based host classifiers consisting of complete (>1000 genes), medium (<100), and small (<20) gene biomarker panels identified COVID-19 disease with 85.1-86.5% accuracy when benchmarked using an independent test set. SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for COVID-19 diagnosis.
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Affiliation(s)
- Dianna L Ng
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lucy M Han
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Jing Cheng
- Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Claudia Sanchez-San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Tony Li
- Department of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Ray Chan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cynthia S Chu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chiara A Wabl
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Debra Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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McClain MT, Constantine FJ, Nicholson BP, Nichols M, Burke TW, Henao R, Jones DC, Hudson LL, Jaggers LB, Veldman T, Mazur A, Park LP, Suchindran S, Tsalik EL, Ginsburg GS, Woods CW. A blood-based host gene expression assay for early detection of respiratory viral infection: an index-cluster prospective cohort study. THE LANCET. INFECTIOUS DISEASES 2020; 21:396-404. [PMID: 32979932 PMCID: PMC7515566 DOI: 10.1016/s1473-3099(20)30486-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/31/2023]
Abstract
Background Early and accurate identification of individuals with viral infections is crucial for clinical management and public health interventions. We aimed to assess the ability of transcriptomic biomarkers to identify naturally acquired respiratory viral infection before typical symptoms are present. Methods In this index-cluster study, we prospectively recruited a cohort of undergraduate students (aged 18–25 years) at Duke University (Durham, NC, USA) over a period of 5 academic years. To identify index cases, we monitored students for the entire academic year, for the presence and severity of eight symptoms of respiratory tract infection using a daily web-based survey, with symptoms rated on a scale of 0–4. Index cases were defined as individuals who reported a 6-point increase in cumulative daily symptom score. Suspected index cases were visited by study staff to confirm the presence of reported symptoms of illness and to collect biospecimen samples. We then identified clusters of close contacts of index cases (ie, individuals who lived in close proximity to index cases, close friends, and partners) who were presumed to be at increased risk of developing symptomatic respiratory tract infection while under observation. We monitored each close contact for 5 days for symptoms and viral shedding and measured transcriptomic responses at each timepoint each day using a blood-based 36-gene RT-PCR assay. Findings Between Sept 1, 2009, and April 10, 2015, we enrolled 1465 participants. Of 264 index cases with respiratory tract infection symptoms, 150 (57%) had a viral cause confirmed by RT-PCR. Of their 555 close contacts, 106 (19%) developed symptomatic respiratory tract infection with a proven viral cause during the observation window, of whom 60 (57%) had the same virus as their associated index case. Nine viruses were detected in total. The transcriptomic assay accurately predicted viral infection at the time of maximum symptom severity (mean area under the receiver operating characteristic curve [AUROC] 0·94 [95% CI 0·92–0·96]), as well as at 1 day (0·87 [95% CI 0·84–0·90]), 2 days (0·85 [0·82–0·88]), and 3 days (0·74 [0·71–0·77]) before peak illness, when symptoms were minimal or absent and 22 (62%) of 35 individuals, 25 (69%) of 36 individuals, and 24 (82%) of 29 individuals, respectively, had no detectable viral shedding. Interpretation Transcriptional biomarkers accurately predict and diagnose infection across diverse viral causes and stages of disease and thus might prove useful for guiding the administration of early effective therapy, quarantine decisions, and other clinical and public health interventions in the setting of endemic and pandemic infectious diseases. Funding US Defense Advanced Research Projects Agency.
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Affiliation(s)
- Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA.
| | - Florica J Constantine
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Lori L Hudson
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - L Brett Jaggers
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Timothy Veldman
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anna Mazur
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lawrence P Park
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Sunil Suchindran
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
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Dong F, He Y, Wang T, Han D, Lu H, Zhao H. Predicting viral exposure response from modeling the changes of co-expression networks using time series gene expression data. BMC Bioinformatics 2020; 21:370. [PMID: 32842958 PMCID: PMC7449007 DOI: 10.1186/s12859-020-03705-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 07/29/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Deciphering the relationship between clinical responses and gene expression profiles may shed light on the mechanisms underlying diseases. Most existing literature has focused on exploring such relationship from cross-sectional gene expression data. It is likely that the dynamic nature of time-series gene expression data is more informative in predicting clinical response and revealing the physiological process of disease development. However, it remains challenging to extract useful dynamic information from time-series gene expression data. RESULTS We propose a statistical framework built on considering co-expression network changes across time from time series gene expression data. It first detects change point for co-expression networks and then employs a Bayesian multiple kernel learning method to predict exposure response. There are two main novelties in our method: the use of change point detection to characterize the co-expression network dynamics, and the use of kernel function to measure the similarity between subjects. Our algorithm allows exposure response prediction using dynamic network information across a collection of informative gene sets. Through parameter estimations, our model has clear biological interpretations. The performance of our method on the simulated data under different scenarios demonstrates that the proposed algorithm has better explanatory power and classification accuracy than commonly used machine learning algorithms. The application of our method to time series gene expression profiles measured in peripheral blood from a group of subjects with respiratory viral exposure shows that our method can predict exposure response at early stage (within 24 h) and the informative gene sets are enriched for pathways related to respiratory and influenza virus infection. CONCLUSIONS The biological hypothesis in this paper is that the dynamic changes of the biological system are related to the clinical response. Our results suggest that when the relationship between the clinical response and a single gene or a gene set is not significant, we may benefit from studying the relationships among genes in gene sets that may lead to novel biological insights.
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Affiliation(s)
- Fangli Dong
- School of Mathematical Sciences, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, 200240, China.,SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, 200240, China
| | - Yong He
- Institute for Financial Studies, Shandong University, No. 27 Shanda South Road, Jinan, 250100, China
| | - Tao Wang
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, 200240, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, 200240, China
| | - Dong Han
- School of Mathematical Sciences, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, 200240, China
| | - Hui Lu
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, 200240, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, 200240, China
| | - Hongyu Zhao
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, 200240, China. .,Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT 06520, USA.
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McClain MT, Constantine FJ, Henao R, Liu Y, Tsalik EL, Burke TW, Steinbrink JM, Petzold E, Nicholson BP, Rolfe R, Kraft BD, Kelly MS, Sempowski GD, Denny TN, Ginsburg GS, Woods CW. Dysregulated transcriptional responses to SARS-CoV-2 in the periphery support novel diagnostic approaches. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.07.20.20155507. [PMID: 32743603 PMCID: PMC7386527 DOI: 10.1101/2020.07.20.20155507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In order to elucidate novel aspects of the host response to SARS-CoV-2 we performed RNA sequencing on peripheral blood samples across 77 timepoints from 46 subjects with COVID-19 and compared them to subjects with seasonal coronavirus, influenza, bacterial pneumonia, and healthy controls. Early SARS-CoV-2 infection triggers a conserved transcriptomic response in peripheral blood that is heavily interferon-driven but also marked by indicators of early B-cell activation and antibody production. Interferon responses during SARS-CoV-2 infection demonstrate unique patterns of dysregulated expression compared to other infectious and healthy states. Heterogeneous activation of coagulation and fibrinolytic pathways are present in early COVID-19, as are IL1 and JAK/STAT signaling pathways, that persist into late disease. Classifiers based on differentially expressed genes accurately distinguished SARS-CoV-2 infection from other acute illnesses (auROC 0.95). The transcriptome in peripheral blood reveals unique aspects of the immune response in COVID-19 and provides for novel biomarker-based approaches to diagnosis.
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Affiliation(s)
- Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
- Durham Veterans Affairs Medical Center, Durham, NC
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC
| | | | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Yiling Liu
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
- Durham Veterans Affairs Medical Center, Durham, NC
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Julie M Steinbrink
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | | | - Robert Rolfe
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC
| | - Bryan D Kraft
- Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University Medical Center, Durham, NC
| | - Matthew S Kelly
- Division of Pediatric Infectious Diseases, Duke University Medical Center
| | | | | | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
- Durham Veterans Affairs Medical Center, Durham, NC
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC
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40
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Ramachandran PS, Wilson MR. Metagenomics for neurological infections - expanding our imagination. Nat Rev Neurol 2020; 16:547-556. [PMID: 32661342 PMCID: PMC7356134 DOI: 10.1038/s41582-020-0374-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
Abstract
Over the past two decades, the diagnosis rate for patients with encephalitis has remained poor despite advances in pathogen-specific testing such as PCR and antigen assays. Metagenomic next-generation sequencing (mNGS) of RNA and DNA extracted from cerebrospinal fluid and brain tissue now offers another strategy for diagnosing neurological infections. Given that mNGS simultaneously assays for a wide range of infectious agents in an unbiased manner, it can identify pathogens that were not part of a neurologist’s initial differential diagnosis either because of the rarity of the infection, because the microorganism has not been previously associated with a clinical phenotype or because it is a newly discovered organism. This Review discusses the technical advantages and pitfalls of cerebrospinal fluid mNGS in the context of patients with neuroinflammatory syndromes, including encephalitis, meningitis and myelitis. We also speculate on how mNGS testing potentially fits into current diagnostic testing algorithms given data on mNGS test performance, cost and turnaround time. Finally, the Review highlights future directions for mNGS technology and other hypothesis-free testing methodologies that are in development. This Review discusses the advantages and pitfalls of metagenomic next-generation sequencing (mNGS) in patients with encephalitis, meningitis and myelitis. The authors outline data on mNGS test performance, cost and turnaround time and highlight future directions for mNGS technology. Meningoencephalitis remains a challenging diagnosis owing to the multitude of possible infectious and autoimmune causes. Meningoencephalitis is associated with a high rate of morbidity and mortality and requires prompt diagnosis and treatment. Metagenomic next-generation sequencing (mNGS) is now a clinically validated test for neuroinfectious diseases that can aid clinicians with a timely diagnosis. mNGS can improve the detection of pathogens that were missed by clinicians or on standard direct testing. mNGS does not perform well when indirect tests are required to make the diagnosis (for example, serology), when infections are compartmentalized and for certain low abundance pathogens. The clinical context of the case is required when interpreting the results of mNGS.
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Affiliation(s)
- Prashanth S Ramachandran
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA. .,Department of Neurology, University of California, San Francisco, CA, USA.
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41
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Gardinassi LG, Souza COS, Sales-Campos H, Fonseca SG. Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse. Front Immunol 2020; 11:1636. [PMID: 32670298 PMCID: PMC7332781 DOI: 10.3389/fimmu.2020.01636] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022] Open
Abstract
The current pandemic of coronavirus disease 19 (COVID-19) has affected millions of individuals and caused thousands of deaths worldwide. The pathophysiology of the disease is complex and mostly unknown. Therefore, identifying the molecular mechanisms that promote progression of the disease is critical to overcome this pandemic. To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. Here, we provide novel perspectives on the pathophysiology of COVID-19 using robust functional approaches to analyze public transcriptome datasets. In addition, we compared the transcriptional signature of COVID-19 patients with individuals infected with SARS-CoV-1 and Influenza A (IAV) viruses. We identified a core transcriptional signature induced by the respiratory viruses in peripheral leukocytes, whereas the absence of significant type I interferon/antiviral responses characterized SARS-CoV-2 infection. We also identified the higher expression of genes involved in metabolic pathways including heme biosynthesis, oxidative phosphorylation and tryptophan metabolism. A BTM-driven meta-analysis of bronchoalveolar lavage fluid (BALF) from COVID-19 patients showed significant enrichment for neutrophils and chemokines, which were also significant in data from lung tissue of one deceased COVID-19 patient. Importantly, our results indicate higher expression of genes related to oxidative phosphorylation both in peripheral mononuclear leukocytes and BALF, suggesting a critical role for mitochondrial activity during SARS-CoV-2 infection. Collectively, these data point for immunopathological features and targets that can be therapeutically exploited to control COVID-19.
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Affiliation(s)
- Luiz G. Gardinassi
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Camila O. S. Souza
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Helioswilton Sales-Campos
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Simone G. Fonseca
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
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Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection. mBio 2020; 11:mBio.01157-20. [PMID: 32546624 PMCID: PMC7298714 DOI: 10.1128/mbio.01157-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Current molecular tests that identify infection with high-consequence viruses such as Ebola virus and Marburg virus are based on the detection of virus material in the blood. These viruses do not undergo significant early replication in the blood and, instead, replicate in organs such as the liver and spleen. Thus, virus begins to accumulate in the blood only after significant replication has already occurred in those organs, making viremia an indicator of infection only after initial stages have become established. Here, we show that a multianalyte assay can correctly identify the infectious agent in nonhuman primates (NHPs) prior to viremia through tracking host infection response transcripts. This illustrates that a single-tube, sample-to-answer format assay could be used to advance the time at which the type of infection can be determined and thereby improve outcomes. Outbreaks of filoviruses, such as those caused by the Ebola (EBOV) and Marburg (MARV) virus, are difficult to detect and control. The initial clinical symptoms of these diseases are nonspecific and can mimic other endemic pathogens. This makes confident diagnosis based on clinical symptoms alone impossible. Molecular diagnostics for these diseases that rely on the detection of viral RNA in the blood are only effective after significant disease progression. As an approach to identify these infections earlier in the disease course, we tested the effectiveness of viral RNA detection combined with an assessment of sentinel host mRNAs that are upregulated following filovirus infection. RNAseq analysis of EBOV-infected nonhuman primates identified host RNAs that are upregulated at early stages of infection. NanoString probes that recognized these host-response RNAs were combined with probes that recognized viral RNA and were used to classify viral infection both prior to viremia and postviremia. This approach was highly successful at identifying samples from nonhuman primate subjects and correctly distinguished the causative agent in a previremic stage in 10 EBOV and 5 MARV samples. This work suggests that unified host response/viral fingerprint assays can enable diagnosis of disease earlier than testing for viral nucleic acid alone, which could decrease transmission events and increase therapeutic effectiveness.
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43
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Credle JJ, Robinson ML, Gunn J, Monaco D, Sie B, Tchir A, Hardick J, Zheng X, Shaw-Saliba K, Rothman RE, Eshleman SH, Pekosz A, Hansen K, Mostafa H, Steinegger M, Larman HB. Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.03.130591. [PMID: 32577648 PMCID: PMC7302202 DOI: 10.1101/2020.06.03.130591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The emergence of SARS-CoV-2 has caused the current COVID-19 pandemic with catastrophic societal impact. Because many individuals shed virus for days before symptom onset, and many show mild or no symptoms, an emergent and unprecedented need exists for development and deployment of sensitive and high throughput molecular diagnostic tests. RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) is a highly multiplexed technology for targeted analysis of polyadenylated mRNA, which incorporates sample barcoding for massively parallel analyses. Here we present a more generalized method, capture RASL-seq ("cRASL-seq"), which enables analysis of any targeted pathogen- (and/or host-) associated RNA molecules. cRASL-seq enables highly sensitive (down to ~1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ~10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid extraction or reverse transcription, steps that have caused testing bottlenecks associated with other assays. Our simplified workflow additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new surveillance technology with the potential to help mitigate the current pandemic and prevent similar public health crises.
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Affiliation(s)
- Joel J. Credle
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan Gunn
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel Monaco
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Brandon Sie
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Alexandra Tchir
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Justin Hardick
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xuwen Zheng
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Kathryn Shaw-Saliba
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard E. Rothman
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Susan H. Eshleman
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kasper Hansen
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Heba Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Martin Steinegger
- Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - H. Benjamin Larman
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
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44
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Steinbrink JM, Zaas AK, Betancourt M, Modliszewski JL, Corcoran DL, McClain MT. A transcriptional signature accurately identifies Aspergillus Infection across healthy and immunosuppressed states. Transl Res 2020; 219:1-12. [PMID: 32165060 PMCID: PMC7170547 DOI: 10.1016/j.trsl.2020.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 12/12/2022]
Abstract
Invasive aspergillosis (IA) is a major cause of critical illness in immunocompromised (IC) patients. However, current fungal tests are limited. Disease-specific gene expression patterns in circulating host cells show promise as novel diagnostics, however it is unknown whether such a 'signature' exists for IA and the effect of iatrogenic immunosuppression on any such biomarkers. Male BALB/c mice were separated into 6 experimental groups based on Aspergillus fumigatus inhalational exposure and IC status (no immunosuppression, cyclophosphamide, and corticosteroids). Mice were sacrificed 4 days postinfection. Whole blood was assayed for transcriptomic responses in peripheral white blood cells via microarray. An elastic net regularized logistic regression was employed to develop classifiers of IA based on gene expression. Aspergillus infection triggers a powerful response in non-IC hosts with 2718 genes differentially expressed between IA and controls. We generated a 146-gene classifier able to discriminate between non-IC infected and uninfected mice with an AUC of 1. However, immunosuppressive medications exhibited a confounding effect on this transcriptomic classifier. After controlling for the genomic effects of immunosuppression, we were able to generate a 187-gene classifier with an AUC of 0.92 in the absence of immunosuppression, 1 with cyclophosphamide, and 0.9 with steroids. The host transcriptomic response to IA is robust and conserved. Pharmacologic perturbation of the host immune response has powerful effects on classifier performance and must be considered when developing such novel diagnostics. When appropriately designed, host-derived peripheral blood transcriptomic responses demonstrate the ability to accurately diagnose Aspergillus infection, even in the presence of immunosuppression.
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Affiliation(s)
- Julie M Steinbrink
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina; Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina.
| | - Aimee K Zaas
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Marisol Betancourt
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina; Augusta University Medical Center, Augusta, Georgia
| | | | - David L Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham North Carolina
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina; Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina; Durham VA Medical Center, Durham, North Carolina
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Yu J, Peterson DR, Baran AM, Bhattacharya S, Wylie TN, Falsey AR, Mariani TJ, Storch GA. Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection. J Infect Dis 2020; 219:1151-1161. [PMID: 30339221 DOI: 10.1093/infdis/jiy608] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Recently there has been a growing interest in the potential for host transcriptomic analysis to augment the diagnosis of infectious diseases. METHODS We compared nasal and blood samples for evaluation of the host transcriptomic response in children with acute respiratory syncytial virus (RSV) infection, symptomatic non-RSV respiratory virus infection, asymptomatic rhinovirus infection, and virus-negative asymptomatic controls. We used nested leave-one-pair-out cross-validation and supervised principal components analysis to define small sets of genes whose expression patterns accurately classified subjects. We validated gene classification scores using an external data set. RESULTS Despite lower quality of nasal RNA, the number of genes detected by microarray in each sample type was equivalent. Nasal gene expression signal derived mainly from epithelial cells but also included a variable leukocyte contribution. The number of genes with increased expression in virus-infected children was comparable in nasal and blood samples, while nasal samples also had decreased expression of many genes associated with ciliary function and assembly. Nasal gene expression signatures were as good or better for discriminating between symptomatic, asymptomatic, and uninfected children. CONCLSUSIONS Our results support the use of nasal samples to augment pathogen-based tests to diagnose viral respiratory infection.
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Affiliation(s)
- Jinsheng Yu
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine, New York
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine, New York
| | - Soumyaroop Bhattacharya
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine, New York
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Ann R Falsey
- Department of Medicine, University of Rochester School of Medicine, New York
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine, New York
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
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Ahn S, Choi H, Lim J, Lee KE. Self-semi-supervised clustering for large scale data with massive null group. J Korean Stat Soc 2020. [DOI: 10.1007/s42952-019-00005-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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47
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Tsalik EL, Khine A, Talebpour A, Samiei A, Parmar V, Burke TW, Mcclain MT, Ginsburg GS, Woods CW, Henao R, Alavie T. Rapid, Sample-to-Answer Host Gene Expression Test to Diagnose Viral Infection. Open Forum Infect Dis 2019; 6:ofz466. [PMID: 34150923 DOI: 10.1093/ofid/ofz466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022] Open
Abstract
Objective Distinguishing bacterial, viral, or other etiologies of acute illness is diagnostically challenging with significant implications for appropriate antimicrobial use. Host gene expression offers a promising approach, although no clinically useful test has been developed yet to accomplish this. Here, Qvella's FAST HR (Richmond Hill, Ontario, Canada) process was developed to quantify previously identified host gene expression signatures in whole blood in <45 minutes. Method Whole blood was collected from 128 human subjects (mean age 47, range 18-88) with clinically adjudicated, microbiologically confirmed viral infection, bacterial infection, noninfectious illness, or healthy controls. Stabilized mRNA was released from cleaned and stabilized RNA-surfactant complexes using e-lysis, an electrical process providing a quantitative real-time reverse transcription polymerase chain reaction-ready sample. Threshold cycle values (CT) for 10 host response targets were normalized to hypoxanthine phosphoribosyltransferase 1 expression, a control mRNA. The transcripts in the signature were specifically chosen to discriminate viral from nonviral infection (bacterial, noninfectious illness, or healthy). Classification accuracy was determined using cross-validated sparse logistic regression. Results Reproducibility of mRNA quantification was within 1 cycle as compared to the difference seen between subjects with viral versus nonviral infection (up to 5.0 normalized CT difference). Classification of 128 subjects into viral or nonviral etiologies demonstrated 90.6% overall accuracy compared to 82.0% for procalcitonin (P = .06). FAST HR achieved rapid and accurate measurement of the host response to viral infection in less than 45 minutes. Conclusions These results demonstrate the ability to translate host gene expression signatures to clinical platforms for use in patients with suspected infection. Clinical Trials Registration NCT00258869.
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Affiliation(s)
- Ephraim L Tsalik
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Ayeaye Khine
- Qvella Corporation, Richmond Hill, Ontario, Canada
| | | | | | - Vilcy Parmar
- Qvella Corporation, Richmond Hill, Ontario, Canada
| | - Thomas W Burke
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah T Mcclain
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medicine Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher W Woods
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medicine Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Ricardo Henao
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Pratt School of Engineering, Duke University, Durham, North Carolina, USA
| | - Tino Alavie
- Qvella Corporation, Richmond Hill, Ontario, Canada
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Carey M, Ramírez JC, Wu S, Wu H. A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection. Stat Methods Med Res 2019; 27:1930-1955. [PMID: 29846143 DOI: 10.1177/0962280217746719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A biological host response to an external stimulus or intervention such as a disease or infection is a dynamic process, which is regulated by an intricate network of many genes and their products. Understanding the dynamics of this gene regulatory network allows us to infer the mechanisms involved in a host response to an external stimulus, and hence aids the discovery of biomarkers of phenotype and biological function. In this article, we propose a modeling/analysis pipeline for dynamic gene expression data, called Pipeline4DGEData, which consists of a series of statistical modeling techniques to construct dynamic gene regulatory networks from the large volumes of high-dimensional time-course gene expression data that are freely available in the Gene Expression Omnibus repository. This pipeline has a consistent and scalable structure that allows it to simultaneously analyze a large number of time-course gene expression data sets, and then integrate the results across different studies. We apply the proposed pipeline to influenza infection data from nine studies and demonstrate that interesting biological findings can be discovered with its implementation.
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Affiliation(s)
- Michelle Carey
- 1 School of Mathematics and Statistics, University College Dublin, Dublin, Ireland
| | - Juan Camilo Ramírez
- 2 Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Hulin Wu
- 2 Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
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Bartholomeus E, De Neuter N, Lemay A, Pattyn L, Tuerlinckx D, Weynants D, Van Lede K, van Berlaer G, Bulckaert D, Boiy T, Vander Auwera A, Raes M, Van der Linden D, Verhelst H, Van Steijn S, Jonckheer T, Dehoorne J, Joos R, Jansens H, Suls A, Van Damme P, Laukens K, Mortier G, Meysman P, Ogunjimi B. Diagnosing enterovirus meningitis via blood transcriptomics: an alternative for lumbar puncture? J Transl Med 2019; 17:282. [PMID: 31443725 PMCID: PMC6708255 DOI: 10.1186/s12967-019-2037-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/18/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Meningitis can be caused by several viruses and bacteria. Identifying the causative pathogen as quickly as possible is crucial to initiate the most optimal therapy, as acute bacterial meningitis is associated with a significant morbidity and mortality. Bacterial meningitis requires antibiotics, as opposed to enteroviral meningitis, which only requires supportive therapy. Clinical presentation is usually not sufficient to differentiate between viral and bacterial meningitis, thereby necessitating cerebrospinal fluid (CSF) analysis by PCR and/or time-consuming bacterial cultures. However, collecting CSF in children is not always feasible and a rather invasive procedure. METHODS In 12 Belgian hospitals, we obtained acute blood samples from children with signs of meningitis (49 viral and 7 bacterial cases) (aged between 3 months and 16 years). After pathogen confirmation on CSF, the patient was asked to give a convalescent sample after recovery. 3' mRNA sequencing was performed to determine differentially expressed genes (DEGs) to create a host transcriptomic profile. RESULTS Enteroviral meningitis cases displayed the largest upregulated fold change enrichment in type I interferon production, response and signaling pathways. Patients with bacterial meningitis showed a significant upregulation of genes related to macrophage and neutrophil activation. We found several significantly DEGs between enteroviral and bacterial meningitis. Random forest classification showed that we were able to differentiate enteroviral from bacterial meningitis with an AUC of 0.982 on held-out samples. CONCLUSIONS Enteroviral meningitis has an innate immunity signature with type 1 interferons as key players. Our classifier, based on blood host transcriptomic profiles of different meningitis cases, is a possible strong alternative for diagnosing enteroviral meningitis.
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Affiliation(s)
- Esther Bartholomeus
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Nicolas De Neuter
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Annelies Lemay
- Department of Paediatrics, AZ Turnhout, Turnhout, Belgium
| | - Luc Pattyn
- Department of Paediatrics, AZ Turnhout, Turnhout, Belgium
| | - David Tuerlinckx
- Université Catholique de Louvain/CHU UCL Namur, Site Dinant, Service de Pédiatrie, Dinant, Belgium
| | - David Weynants
- Department of Paediatrics, CHU ULC Namur Ste Elisabeth, Namur, Belgium
| | - Koen Van Lede
- Department of Paediatrics, AZ Nikolaas, Sint-Niklaas, Belgium
| | - Gerlant van Berlaer
- Department of Emergency Medicine/Pediatric Care, University Hospital Brussels, Jette, Belgium
| | - Dominique Bulckaert
- Department of Emergency Medicine/Pediatric Care, University Hospital Brussels, Jette, Belgium
| | - Tine Boiy
- Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium
| | | | - Marc Raes
- Department of Paediatrics, Jessa Hospital, Hasselt, Belgium
| | - Dimitri Van der Linden
- Paediatric Infectious Diseases, Department of Paediatrics, CHU ULC Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | - Helene Verhelst
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium
| | | | - Tijl Jonckheer
- Department of Paediatrics, GZA Sint-Vincentius, Antwerp, Belgium
| | - Joke Dehoorne
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium
| | - Rik Joos
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium.,Antwerp Center for Paediatric Rheumatology and AutoInflammatory Diseases, Antwerp, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Arvid Suls
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Pieter Meysman
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium. .,Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium. .,Antwerp Center for Paediatric Rheumatology and AutoInflammatory Diseases, Antwerp, Belgium. .,Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium. .,Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, 00323/8213251, Antwerp, Belgium. .,Department of Pediatrics, University Hospital Brussels, Jette, Belgium.
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50
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Tang BM, Shojaei M, Teoh S, Meyers A, Ho J, Ball TB, Keynan Y, Pisipati A, Kumar A, Eisen DP, Lai K, Gillett M, Santram R, Geffers R, Schreiber J, Mozhui K, Huang S, Parnell GP, Nalos M, Holubova M, Chew T, Booth D, Kumar A, McLean A, Schughart K. Neutrophils-related host factors associated with severe disease and fatality in patients with influenza infection. Nat Commun 2019; 10:3422. [PMID: 31366921 PMCID: PMC6668409 DOI: 10.1038/s41467-019-11249-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 06/28/2019] [Indexed: 11/09/2022] Open
Abstract
Severe influenza infection has no effective treatment available. One of the key barriers to developing host-directed therapy is a lack of reliable prognostic factors needed to guide such therapy. Here, we use a network analysis approach to identify host factors associated with severe influenza and fatal outcome. In influenza patients with moderate-to-severe diseases, we uncover a complex landscape of immunological pathways, with the main changes occurring in pathways related to circulating neutrophils. Patients with severe disease display excessive neutrophil extracellular traps formation, neutrophil-inflammation and delayed apoptosis, all of which have been associated with fatal outcome in animal models. Excessive neutrophil activation correlates with worsening oxygenation impairment and predicted fatal outcome (AUROC 0.817-0.898). These findings provide new evidence that neutrophil-dominated host response is associated with poor outcomes. Measuring neutrophil-related changes may improve risk stratification and patient selection, a critical first step in developing host-directed immune therapy.
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Affiliation(s)
- Benjamin M Tang
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia. .,Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia. .,Respiratory Tract Infection Research Node, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia.
| | - Maryam Shojaei
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia.,Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia
| | - Sally Teoh
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Adrienne Meyers
- National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - John Ho
- National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - T Blake Ball
- National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Yoav Keynan
- Department of Internal Medicine, Medical Microbiology and Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Amarnath Pisipati
- Department of Chemistry and Biological Chemistry, Harvard University, Cambridge, MA, USA
| | - Aseem Kumar
- Department of Chemistry and Biochemistry, Laurentian University, Laurentian, Canada
| | - Damon P Eisen
- Townsville Hospital, Townsville, Queensland, Australia
| | - Kevin Lai
- Department of Emergency Medicine, Westmead Hospital, Sydney, Australia
| | - Mark Gillett
- Department of Emergency Medicine, Royal North Shore Hospital, Sydney, Australia
| | - Rahul Santram
- Department of Emergency Medicine, St. Vincent Hospital, Sydney, Australia
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jens Schreiber
- Otto-von-Guerike University of Magdeburg, Clinic of Pneumology, Magdeburg, Germany
| | - Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Centre, Memphis, TN, USA
| | - Stephen Huang
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia
| | - Marek Nalos
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia.,Department of Internal Medicine, Medical Faculty Plzen, Charles University Prague, Staré Město, Czech Republic
| | - Monika Holubova
- Biomedical Centre, Medical Faculty Plzen, Charles University Prague, Staré Město, Czech Republic
| | - Tracy Chew
- Sydney Informatic Hub, The University of Sydney, Sydney, Australia
| | - David Booth
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia
| | - Anand Kumar
- Section of Critical Care Medicine and Section of Infectious Diseases, Departments of Medicine, Medical Microbiology and Pharmacology, University of Manitoba, Winnipeg, Canada
| | - Anthony McLean
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,University of Veterinary Medicine, Hannover, Germany.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Centre, Memphis, TN, USA
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