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Xie L, Zhu G, Long S, Wang M, Cheng X, Dong Y, Wang C, Wang G. Identification of MORN3 and LLGL2 as novel diagnostic biomarkers for latent tuberculosis infection using machine learning strategies and experimental verification. Ann Med 2024; 56:2380797. [PMID: 39054612 DOI: 10.1080/07853890.2024.2380797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/10/2024] [Accepted: 05/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Current diagnostic methods cannot effectively distinguish between latent tuberculosis infection (LTBI) and active tuberculosis (ATB). This study aims to explore novel non-invasive diagnostic biomarkers for LTBI and to elucidate possible molecular mechanisms of LTBI pathogenesis. METHODS Three GEO datasets (GSE19439, GSE19444, and GSE62525) were utilized to analyze the differentially expressed genes (DEGs). Functional enrichment studies were then performed on these DEGs. To ascertain potential diagnostic biomarkers, we utilized two different machine learning techniques: LASSO and RF. ROC curves were constructed in both the training and validation datasets to assess the diagnostic efficacy. The expression of identified biomarkers was verified by RT-qPCR in our own Chinese cohort. Using CIBERSORT, we estimated the abundances of 22 immune cell types in LTBI group, and subsequently analyzed the relationship between biomarker expression and immune cell infiltration. RESULTS 166 DEGs were identified between ATB and LTBI groups, which are primarily associated with immune responses, inflammatory signaling pathways, and infection factors. Following that, 22 candidate diagnostic biomarkers for LTBI were selected in the machine learning process. Three up-regulated genes, MORN3, LLGL2, and IFT140, whose expression levels were not previously reported in TB, were validated using the training and validation cohort datasets. In our own Chinese cohort, we also found that MORN3 and LLGL2 showed good diagnostic effect using RT-qPCR method. Finally, we revealed the specific infiltration features of immune cells in LTBI and observed a notable correlation between potential marker expression and immune cells. CONCLUSIONS MORN3 and LLGL2 emerged as candidate diagnostic biomarkers for LTBI, following the elucidation of the key immune cell types involved. Our findings will contribute to providing a potential target for early noninvasive diagnosis of LTBI patients.
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Affiliation(s)
- Longxiang Xie
- Department of General Surgery, Huaihe Hospital of Henan University, Henan University, Kaifeng, Henan, China
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
| | - Gaoya Zhu
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
| | - Sibo Long
- Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Mengna Wang
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
| | - Xinxin Cheng
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
| | - Yuzhe Dong
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
| | - Chaoyang Wang
- Department of General Surgery, Huaihe Hospital of Henan University, Henan University, Kaifeng, Henan, China
| | - Guirong Wang
- Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
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Leo S, Narasimhan M, Rathinam S, Banerjee A. Biomarkers in diagnosing and therapeutic monitoring of tuberculosis: a review. Ann Med 2024; 56:2386030. [PMID: 39097795 PMCID: PMC11299445 DOI: 10.1080/07853890.2024.2386030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/06/2024] [Accepted: 06/12/2024] [Indexed: 08/05/2024] Open
Abstract
Tuberculosis (TB) continues to pose a significant health challenge worldwide, emphasizing the importance of prompt diagnosis and efficient monitoring of treatment outcomes for effective disease control. Biomarkers have become increasingly important in the realm of TB diagnoses and treatment. The objective of this comprehensive review is to examine the present state of biomarkers employed in the diagnosis of TB, monitoring the response to treatment, and predicting treatment outcomes. In this study, we undertake a comprehensive examination of the diverse biomarkers utilized in TB diagnoses, spanning molecular, immunological, and other novel methodologies. Furthermore, we examine the potential of biomarkers in the context of therapeutic monitoring, assessment of treatment effectiveness, and anticipation of drug resistance. Additionally, this paper presents future prospects regarding the utilization of biomarkers in the therapy of tuberculosis.
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Affiliation(s)
- Sneha Leo
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Meenakshi Narasimhan
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Sridhar Rathinam
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Antara Banerjee
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
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López-Suárez A, Santos-Sebastián M, Hernanz-Lobo A, Rincón-López E, Aguilera-Alonso D, Saavedra-Lozano J, Ruiz Serrano MJ, Hernández-Bartolomé Á, Medrano de Dios LM, Jiménez Fuentes JL, Navarro ML, Tebruegge M, Santiago-García B. Diagnostic potential of combining plasma biomarkers of tissue damage and inflammation in pediatric TB. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024:S1684-1182(24)00122-1. [PMID: 39271436 DOI: 10.1016/j.jmii.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/31/2024] [Accepted: 07/22/2024] [Indexed: 09/15/2024]
Abstract
INTRODUCTION Immune-based diagnostic tests for tuberculosis (TB) have suboptimal sensitivity in children and cannot differentiate between latent infection (LTBI) and active disease. This study evaluated the diagnostic potential of a broad range of biomarkers of tissue damage and inflammation in unstimulated plasma in children. METHODS We analyzed 17 biomarkers in 15 non-M. tuberculosis (MTB)-infected controls and 33 children with TB infection (LTBI, n = 8; probable TB, n = 19; confirmed TB, n = 6). Biomarker concentrations were measured using a Luminex magnetic bead-based platform and multiplex sandwich immunoassays. Concentrations, correlations and diagnostic accuracy assessments were conducted among patient groups. RESULTS Confirmed TB cases had significantly higher concentrations of IFN-γ and IL-2 and higher IFN-γ/MCP-1 and IL-2/MCP-1 ratios compared to LTBI and non-MTB-infected children. Among children with confirmed TB, there was a strong correlation between IFN-γ and IL-10 (r = 0.95; p < 0.001) and a significant correlation between IL-2 and IL-1ra (r = 0.92), IL-21 (r = 0.91), MCP-3 (r = 0.84), and MMP-1 (r = 0.85). The IFN-γ/MCP-1 ratio was the most accurate biomarker combination for differentiating between MTB-infected and non-MTB-infected children (AUC, 0.82; sensitivity, 87.9%; specificity, 66.6%; p < 0.001) and between active TB and non-MTB-infected children (AUC 0.82; sensitivity 88.0%; specificity 60.0%; p < 0.001). None of the biomarkers investigated were able to discriminate between LTBI and active TB. CONCLUSION Our data suggest that combining the analyses of multiple biomarkers in plasma has the potential to enhance diagnosis of TB in children and, thus, warrants additional investigation. In particular, the diagnostic potential of IFN-γ/MCP-1 ratios should be further explored in larger pediatric cohorts.
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Affiliation(s)
- Andrea López-Suárez
- Pediatric Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain.
| | - Mar Santos-Sebastián
- Pediatric Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain; Gregorio Marañón Research Health Institute (IiSGM), Madrid, Spain
| | - Alicia Hernanz-Lobo
- Pediatric Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Elena Rincón-López
- Pediatric Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain; Gregorio Marañón Research Health Institute (IiSGM), Madrid, Spain
| | - David Aguilera-Alonso
- Pediatric Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain; Gregorio Marañón Research Health Institute (IiSGM), Madrid, Spain
| | - Jesús Saavedra-Lozano
- Pediatric Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain; Gregorio Marañón Research Health Institute (IiSGM), Madrid, Spain
| | - María Jesús Ruiz Serrano
- Microbiology and Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Respiratory Diseases (CIBERES), Carlos III Health Institute, Madrid, Spain
| | | | - Luz María Medrano de Dios
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis Jiménez Fuentes
- Gregorio Marañón Research Health Institute (IiSGM), Madrid, Spain; Laboratory Platform (Immunology), General Universitary Hospital Gregorio Marañon (HGUGM), Madrid, 28007, Spain; Spanish HIV HGM BioBank, Madrid, 28007, Spain
| | - María Luisa Navarro
- Pediatric Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain; Gregorio Marañón Research Health Institute (IiSGM), Madrid, Spain
| | - Marc Tebruegge
- Department of Infection, Immunity & Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Paediatrics and National Reference Centre for Paediatric Tuberculosis, Klinik Ottakring, Wiener Gesundheitsverbund, Vienna, Austria; Department of Paediatrics, Royal Children's Hospital Melbourne, University of Melbourne, Melbourne, Australia
| | - Begoña Santiago-García
- Pediatric Infectious Diseases Department, Gregorio Marañón University Hospital, Madrid, Spain; Biomedical Research Centre Network for Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain; Gregorio Marañón Research Health Institute (IiSGM), Madrid, Spain
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Sybertz NM, Al Jubaer S, Larsen MH, Alexander KA. Assessment of transcriptional markers for the differentiation of Mycobacterium mungi infection status in free-ranging banded mongoose (Mungos mungo). Tuberculosis (Edinb) 2024; 149:102565. [PMID: 39293135 DOI: 10.1016/j.tube.2024.102565] [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: 06/01/2024] [Revised: 08/14/2024] [Accepted: 09/04/2024] [Indexed: 09/20/2024]
Abstract
There is an increasingly urgent need to improve our ability to accurately forecast and control zoonotic diseases in wildlife reservoirs. We are confronted, however, with the continued challenge of accurately determining host infection status across space and time. This dilemma is epitomized with the Mycobacterium tuberculosis Complex (MTBC) pathogens and particularly in free-ranging wildlife, a critical global challenge for both human and animal health. In humans, transcriptional markers have been increasingly identified as a robust tool for diagnosing Mycobacterium tuberculosis (MTB) infection status but have rarely been utilized for diagnosing TB in free-ranging wildlife populations. Here, we report the first use of transcriptional markers to evaluate TB infection status in a free-ranging wildlife species, banded mongoose (Mungos mungo), infected with the MTBC pathogen, Mycobacterium mungi. In this study, we found that GBP5 and DUSP3 were significantly upregulated in free-ranging banded mongoose infected with M. mungi. These results provide the first step in developing an antemortem diagnostic tool for use in free-ranging wildlife species. Our results highlight the potential of transcriptional marker-based assays to advance our ability to detect and manage TB in free-ranging wildlife, especially in field studies and other scenarios when conventional diagnostics are not feasible.
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Affiliation(s)
- Nicholas M Sybertz
- Department of Fish and Wildlife Conservation, Virginia Tech, 310 West Campus Drive, Blacksburg, VA, USA.
| | - Shamim Al Jubaer
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, USA.
| | - Michelle H Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, USA.
| | - Kathleen A Alexander
- Department of Fish and Wildlife Conservation, Virginia Tech, 310 West Campus Drive, Blacksburg, VA, USA; Chobe Research Institute, Center for African Resources: Communities, Animals, and Land Use (CARACAL), Plot 3102 Airport Road, Kasane, Botswana.
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Channon-Wells S, Habgood-Coote D, Vito O, Galassini R, Wright VJ, Brent AJ, Heyderman RS, Anderson ST, Eley B, Martinón-Torres F, Levin M, Kaforou M, Herberg JA. Integration and validation of host transcript signatures, including a novel 3-transcript tuberculosis signature, to enable one-step multiclass diagnosis of childhood febrile disease. J Transl Med 2024; 22:802. [PMID: 39210372 PMCID: PMC11360490 DOI: 10.1186/s12967-024-05241-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/27/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Whole blood host transcript signatures show great potential for diagnosis of infectious and inflammatory illness, with most published signatures performing binary classification tasks. Barriers to clinical implementation include validation studies, and development of strategies that enable simultaneous, multiclass diagnosis of febrile illness based on gene expression. METHODS We validated five distinct diagnostic signatures for paediatric infectious diseases in parallel using a single NanoString nCounter® experiment. We included a novel 3-transcript signature for childhood tuberculosis, and four published signatures which differentiate bacterial infection, viral infection, or Kawasaki disease from other febrile illnesses. Signature performance was assessed using receiver operating characteristic curve statistics. We also explored conceptual frameworks for multiclass diagnostic signatures, including additional transcripts found to be significantly differentially expressed in previous studies. Relaxed, regularised logistic regression models were used to derive two novel multiclass signatures: a mixed One-vs-All model (MOVA), running multiple binomial models in parallel, and a full-multiclass model. In-sample performance of these models was compared using radar-plots and confusion matrix statistics. RESULTS Samples from 91 children were included in the study: 23 bacterial infections (DB), 20 viral infections (DV), 14 Kawasaki disease (KD), 18 tuberculosis disease (TB), and 16 healthy controls. The five signatures tested demonstrated cross-platform performance similar to their primary discovery-validation cohorts. The signatures could differentiate: KD from other diseases with area under ROC curve (AUC) of 0.897 [95% confidence interval: 0.822-0.972]; DB from DV with AUC of 0.825 [0.691-0.959] (signature-1) and 0.867 [0.753-0.982] (signature-2); TB from other diseases with AUC of 0.882 [0.787-0.977] (novel signature); TB from healthy children with AUC of 0.910 [0.808-1.000]. Application of signatures outside of their designed context reduced performance. In-sample error rates for the multiclass models were 13.3% for the MOVA model and 0.0% for the full-multiclass model. The MOVA model misclassified DB cases most frequently (18.7%) and TB cases least (2.7%). CONCLUSIONS Our study demonstrates the feasibility of NanoString technology for cross-platform validation of multiple transcriptomic signatures in parallel. This external cohort validated performance of all five signatures, including a novel sparse TB signature. Two exploratory multi-class models showed high potential accuracy across four distinct diagnostic groups.
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Affiliation(s)
- Samuel Channon-Wells
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Dominic Habgood-Coote
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Ortensia Vito
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Rachel Galassini
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Victoria J Wright
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Andrew J Brent
- Oxford University Hospitals NHS Foundation Trust, Headley Way, Headington, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | | | - Brian Eley
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines, Infections and Pediatrics Research Group (GENVIP), Instituto de Investigación Santiaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Instituto de Salud Carlos III, Madrid, Spain
| | - Michael Levin
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Jethro A Herberg
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK.
- Centre for Paediatrics and Child Health, Imperial College London, London, UK.
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Muwanga VM, Mendelsohn SC, Leukes V, Stanley K, Mbandi SK, Erasmus M, Flinn M, Fisher TL, Raphela R, Bilek N, Malherbe ST, Tromp G, Van Der Spuy G, Walzl G, Chegou NN, Scriba TJ. Blood transcriptomic signatures for symptomatic tuberculosis in an African multicohort study. Eur Respir J 2024; 64:2400153. [PMID: 38964778 PMCID: PMC11325265 DOI: 10.1183/13993003.00153-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND Multiple host blood transcriptional signatures have been developed as non-sputum triage tests for tuberculosis (TB). We aimed to compare the diagnostic performance of 20 blood transcriptomic TB signatures for differentiating between symptomatic patients who have TB versus other respiratory diseases (ORD). METHODS As part of a nested case-control study, individuals presenting with respiratory symptoms at primary healthcare clinics in Ethiopia, Malawi, Namibia, Uganda, South Africa and The Gambia were enrolled. TB was diagnosed based on clinical, microbiological and radiological findings. Transcriptomic signatures were measured in whole blood using microfluidic real-time quantitative PCR. Diagnostic performance was benchmarked against the World Health Organization Target Product Profile (TPP) for a non-sputum TB triage test. RESULTS Among 579 participants, 158 had definite, microbiologically confirmed TB, 32 had probable TB, while 389 participants had ORD. Nine signatures differentiated between ORD and TB with equivalent performance (Satproedprai7: area under the curve 0.83 (95% CI 0.79-0.87); Jacobsen3: 0.83 (95% CI 0.79-0.86); Suliman2: 0.82 (95% CI 0.78-0.86); Roe1: 0.82 (95% CI 0.78-0.86); Kaforou22: 0.82 (95% CI 0.78-0.86); Sambarey10: 0.81 (95% CI 0.77-0.85); Duffy9: 0.81 (95% CI 0.76-0.86); Gliddon3: 0.8 (95% CI 0.75-0.85); Suliman4 0.79 (95% CI 0.75-0.84)). Benchmarked against a 90% sensitivity, these signatures achieved specificities between 44% (95% CI 38-49%) and 54% (95% CI 49-59%), not meeting the TPP criteria. Signature scores significantly varied by HIV status and country. In country-specific analyses, several signatures, such as Satproedprai7 and Penn-Nicholson6, met the minimal TPP criteria for a triage test in Ethiopia, Malawi and South Africa. CONCLUSION No signatures met the TPP criteria in a pooled analysis of all countries, but several signatures met the minimum criteria for a non-sputum TB triage test in some countries.
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Affiliation(s)
- Vanessa Mwebaza Muwanga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Vinzeigh Leukes
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kim Stanley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mzwandile Erasmus
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Marika Flinn
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tarryn-Lee Fisher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Rodney Raphela
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Stephanus T Malherbe
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gian Van Der Spuy
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Novel N Chegou
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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Krishnan P, Bobak CA, Hill JE. Sex-specific blood-derived RNA biomarkers for childhood tuberculosis. Sci Rep 2024; 14:16859. [PMID: 39039071 PMCID: PMC11263679 DOI: 10.1038/s41598-024-66946-6] [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: 04/07/2024] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Confirmatory diagnosis of childhood tuberculosis (TB) remains a challenge mainly due to its dependence on sputum samples and the paucibacillary nature of the disease. Thus, only ~ 30% of suspected cases in children are diagnosed and the need for minimally invasive, non-sputum-based biomarkers remains unmet. Understanding host molecular changes by measuring blood-based transcriptomic markers has shown promise as a diagnostic tool for TB. However, the implication of sex contributing to disease heterogeneity and therefore diagnosis remains to be understood. Using publicly available gene expression data (GSE39939, GSE39940; n = 370), we report a sex-specific RNA biomarker signature that could improve the diagnosis of TB disease in children. We found four gene biomarker signatures for male (SLAMF8, GBP2, WARS, and FCGR1C) and female pediatric patients (GBP6, CELSR3, ALDH1A1, and GBP4) from Kenya, South Africa, and Malawi. Both signatures achieved a sensitivity of 85% and a specificity of 70%, which approaches the WHO-recommended target product profile for a triage test. Our gene signatures outperform most other gene signatures reported previously for childhood TB diagnosis.
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Affiliation(s)
- Preethi Krishnan
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Carly A Bobak
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, 03755, USA
| | - Jane E Hill
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, V6T 1Z3, Canada.
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8
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Reid VA, Ramos EI, Veerapandian R, Carmona A, Gadad SS, Dhandayuthapani S. Differential Expression of lncRNAs in HIV Patients with TB and HIV-TB with Anti-Retroviral Treatment. Noncoding RNA 2024; 10:40. [PMID: 39051374 PMCID: PMC11270221 DOI: 10.3390/ncrna10040040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/26/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Tuberculosis (TB) is the leading cause of death among people with HIV-1 infection. To improve the diagnosis and treatment of HIV-TB patients, it is important to understand the mechanisms underlying these conditions. Here, we used an integrated genomics approach to analyze and determine the lncRNAs that are dysregulated in HIV-TB patients and HIV-TB patients undergoing anti-retroviral therapy (ART) using a dataset available in the public domain. The analyses focused on the portion of the genome transcribed into non-coding transcripts, which historically have been poorly studied and received less focus. This revealed that Mtb infection in HIV prominently up-regulates the expression of long non-coding RNA (lncRNA) genes DAAM2-AS1, COL4A2-AS1, LINC00599, AC008592.1, and CLRN1-AS1 and down-regulates the expression of lncRNAs AC111000.4, AC100803.3, AC016168.2, AC245100.7, and LINC02073. It also revealed that ART down-regulates the expression of some lncRNA genes (COL4A2-AS1, AC079210.1, MFA-AS1, and LINC01993) that are highly up-regulated in HIV-TB patients. Furthermore, the interrogation of the genomic regions that are associated with regulated lncRNAs showed enrichment for biological processes linked to immune pathways in TB-infected conditions. However, intriguingly, TB patients treated with ART showed completely opposite and non-overlapping pathways. Our findings suggest that lncRNAs could be used to identify critical diagnostic, prognostic, and treatment targets for HIV-TB patients.
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Affiliation(s)
- Victoria A. Reid
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA;
| | - Enrique I. Ramos
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA;
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Raja Veerapandian
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
| | - Areanna Carmona
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
| | - Shrikanth S. Gadad
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA;
- Frederick L. Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA
| | - Subramanian Dhandayuthapani
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA;
- Frederick L. Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA
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9
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Kreitmann L, D'Souza G, Miglietta L, Vito O, Jackson HR, Habgood-Coote D, Levin M, Holmes A, Kaforou M, Rodriguez-Manzano J. A computational framework to improve cross-platform implementation of transcriptomics signatures. EBioMedicine 2024; 105:105204. [PMID: 38901146 PMCID: PMC11245942 DOI: 10.1016/j.ebiom.2024.105204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/29/2024] [Accepted: 06/02/2024] [Indexed: 06/22/2024] Open
Abstract
The emergence of next-generation sequencing technologies and computational advances have expanded our understanding of gene expression regulation (i.e., the transcriptome). This has also led to an increased interest in using transcriptomic biomarkers to improve disease diagnosis and stratification, to assess prognosis and predict the response to treatment. Significant progress in identifying transcriptomic signatures for various clinical needs has been made, with large discovery studies accounting for challenges such as patient variability, unwanted batch effects, and data complexities; however, obstacles related to the technical aspects of cross-platform implementation still hinder the successful integration of transcriptomic technologies into standard diagnostic workflows. In this article, we discuss the challenges associated with integrating transcriptomic signatures derived using high-throughput technologies (such as RNA-sequencing) into clinical diagnostic tools using nucleic acid amplification (NAA) techniques. The novelty of the proposed approach lies in our aim to embed constraints related to cross-platform implementation in the process of signature discovery. These constraints could include technical limitations of amplification platform and chemistry, the maximal number of targets imposed by the chosen multiplexing strategy, and the genomic context of identified RNA biomarkers. Finally, we propose to build a computational framework that would integrate these constraints in combination with existing statistical and machine learning models used for signature identification. We envision that this could accelerate the integration of RNA signatures discovered by high-throughput technologies into NAA-based approaches suitable for clinical applications.
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Affiliation(s)
- Louis Kreitmann
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Giselle D'Souza
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Luca Miglietta
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Ortensia Vito
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Heather R Jackson
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Dominic Habgood-Coote
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Michael Levin
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Alison Holmes
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, W2 1NY, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, London, W2 1NY, United Kingdom
| | - Jesus Rodriguez-Manzano
- Section of Adult Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom; Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom.
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10
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Zhang P, Zheng J, Han T, Ma J, Gnanashanmugam D, Li M, Tang YW, Deng G. A blood-based 3-gene signature score for therapeutic monitoring in patients with pulmonary tuberculosis. Tuberculosis (Edinb) 2024; 147:102521. [PMID: 38801793 DOI: 10.1016/j.tube.2024.102521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
OBJECTIVE To assess the validity of Xpert Tuberculosis Fingerstick score for monitoring treatment response and analyze factors influencing its performance. METHODS 122 adults with pulmonary tuberculosis were recruited and stratified into three cohorts: Diabetic-drug-susceptible-TB (DM-TB), Non-diabetic-drug-susceptible-TB (NDM-TB) and Non-diabetic Multidrug-resistant TB (MDR-TB). Fingerstick blood specimens were tested at treatment initiation (M0) and the end of the first (M1), second (M2), and sixth month (M6) to generate a TB-score. RESULTS The TB-score in all participants yielded an AUC of 0.707 (95% CI: 0.579-0.834) at M2 when its performance was evaluated against sputum culture conversion. In all non-diabetes patients, the AUC reached 0.88 (95% CI: 0.756-1.000) with an optimal cut-off value of 1.95 at which sensitivity was 90.0% (95% CI: 59.6-98.2%) and specificity was 81.3% (95% CI: 70.0-88.9%). The mean TB score was higher in patients with low bacterial loads (n = 31) than those with high bacterial loads (n = 91) at M0, M1, M2, and M6, and was higher in non-cavitary patients (n = 71) than those with cavitary lesions (n = 51) at M0, M1, and M2. CONCLUSION Xpert TB-score shows promising predictive value for culture conversion in non-diabetic TB patients. Sputum bacterial load and lung cavitation status have an influence on the value of TB score.
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Affiliation(s)
- Peize Zhang
- Department of Pulmonary Medicine and Tuberculosis, The Third People's Hospital of Shenzhen, China.
| | - Junfeng Zheng
- Department of Pulmonary Medicine and Tuberculosis, The Third People's Hospital of Shenzhen, China.
| | - Tingting Han
- Guangdong Medical University, The First Clinical Medical College, Zhanjiang, Guangdong, China.
| | - Jian Ma
- Medical Affairs, Danaher Corporation/Cepheid (China), Shanghai, China.
| | | | - Mengran Li
- Department of Biostatistics & Data Management, Beckman Coulter, Shanghai, China.
| | - Yi-Wei Tang
- Medical Affairs, Danaher Corporation/Cepheid (China), Shanghai, China.
| | - Guofang Deng
- Department of Pulmonary Medicine and Tuberculosis, The Third People's Hospital of Shenzhen, China.
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11
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Rodrigues C, Singhal T. What is New in the Diagnosis of Childhood Tuberculosis? Indian J Pediatr 2024; 91:717-723. [PMID: 38163830 DOI: 10.1007/s12098-023-04992-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
The fact that almost half of the 1 million cases of childhood tuberculosis (TB) globally remain undiagnosed jeopardizes the TB elimination goal. Fortunately, there are new advances in this field which have the potential to bridge this diagnostic gap. Advances in imaging include computer assisted interpretation of chest X-rays (CXRs), point of care ultrasound (POCUS) and faster and superior computed tomography/ magnetic resonance imaging (CT/ MRI) protocols. The urine lipoarabinomannan test has proved to be a good point of care test for diagnosing TB in Human immunodeficiency virus (HIV) infected children. Stool and nasopharyngeal aspirates are emerging as acceptable alternatives for gastric lavage and induced sputum for diagnosing intrathoracic tuberculosis. Xpert MTB/RIF Ultra has improved sensitivity compared to Xpert MTB/RIF for diagnosing both pulmonary/ extrapulmonary TB. Xpert XDR is another commercially available accurate point of care test for detecting resistance to drugs other than rifampicin in smear positive samples. Other molecular methods including new line probe assays, pyrosequencing, whole genome sequencing, and targeted next generation sequencing are extremely promising but not available commercially at present. The C-Tb skin test is an acceptable alternative to the tuberculin skin test and interferon gamma release assays for diagnosis of latent infection. There is an urgent need to incorporate some of these advances in the existing diagnostic algorithms of childhood TB.
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Affiliation(s)
- Camilla Rodrigues
- Department of Microbiology & Infection Prevention Control, Hinduja Hospital, Mahim, Mumbai, India
| | - Tanu Singhal
- Department of Pediatrics and Infectious Disease, Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute, Mumbai, India.
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12
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Wang X, VanValkenberg A, Odom AR, Ellner JJ, Hochberg NS, Salgame P, Patil P, Johnson WE. Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures. BMC Infect Dis 2024; 24:610. [PMID: 38902649 PMCID: PMC11191245 DOI: 10.1186/s12879-024-09457-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease. However, an unresolved issue is whether gene set enrichment analysis of the signature transcripts alone is sufficient for prediction and differentiation or whether it is necessary to use the original model created when the signature was derived. Intra-method comparison is complicated by the unavailability of original training data and missing details about the original trained model. To facilitate the utilization of these signatures in TB research, comparisons between gene set scoring methods cross-data validation of original model implementations are needed. METHODS We compared the performance of 19 TB gene signatures across 24 transcriptomic datasets using both rrebuilt original models and gene set scoring methods. Existing gene set scoring methods, including ssGSEA, GSVA, PLAGE, Singscore, and Zscore, were used as alternative approaches to obtain the profile scores. The area under the ROC curve (AUC) value was computed to measure performance. Correlation analysis and Wilcoxon paired tests were used to compare the performance of enrichment methods with the original models. RESULTS For many signatures, the predictions from gene set scoring methods were highly correlated and statistically equivalent to the results given by the original models. In some cases, PLAGE outperformed the original models when considering signatures' weighted mean AUC values and the AUC results within individual studies. CONCLUSION Gene set enrichment scoring of existing gene sets can distinguish patients with active TB disease from other clinical conditions with equivalent or improved accuracy compared to the original methods and models. These data justify using gene set scoring methods of published TB gene signatures for predicting TB risk and treatment outcomes, especially when original models are difficult to apply or implement.
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Affiliation(s)
- Xutao Wang
- Department of Biostatistics, Boston University, Boston, MA, USA
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Arthur VanValkenberg
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Aubrey R Odom
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Jerrold J Ellner
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Natasha S Hochberg
- Boston Medical Center, Boston, MA, USA
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, USA
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Prasad Patil
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - W Evan Johnson
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, USA.
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA.
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13
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Li L, Wang T, Chen Z, Liang J, Ding H. Multi-cohort analysis reveals immune subtypes and predictive biomarkers in tuberculosis. Sci Rep 2024; 14:13345. [PMID: 38858405 PMCID: PMC11164950 DOI: 10.1038/s41598-024-63365-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
Tuberculosis (TB) remains a significant global health threat, necessitating effective strategies for diagnosis, prognosis, and treatment. This study employs a multi-cohort analysis approach to unravel the immune microenvironment of TB and delineate distinct subtypes within pulmonary TB (PTB) patients. Leveraging functional gene expression signatures (Fges), we identified three PTB subtypes (C1, C2, and C3) characterized by differential immune-inflammatory activity. These subtypes exhibited unique molecular features, functional disparities, and cell infiltration patterns, suggesting varying disease trajectories and treatment responses. A neural network model was developed to predict PTB progression based on a set of biomarker genes, achieving promising accuracy. Notably, despite both genders being affected by PTB, females exhibited a relatively higher risk of deterioration. Additionally, single-cell analysis provided insights into enhanced major histocompatibility complex (MHC) signaling in the rapid clearance of early pathogens in the C3 subgroup. This comprehensive approach offers valuable insights into PTB pathogenesis, facilitating personalized treatment strategies and precision medicine interventions.
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Affiliation(s)
- Ling Li
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China
| | - Tao Wang
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China
| | - Zhi Chen
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China
| | - Jianqin Liang
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China
| | - Hong Ding
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China.
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14
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Dungu KHS, Carlsen ELM, Glenthøj JP, Schmidt LS, Jørgensen IM, Cortes D, Poulsen A, Vissing NH, Bagger FO, Nygaard U. Host RNA Expression Signatures in Young Infants with Urinary Tract Infection: A Prospective Study. Int J Mol Sci 2024; 25:4857. [PMID: 38732074 PMCID: PMC11084417 DOI: 10.3390/ijms25094857] [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: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Early diagnosis of infections in young infants remains a clinical challenge. Young infants are particularly vulnerable to infection, and it is often difficult to clinically distinguish between bacterial and viral infections. Urinary tract infection (UTI) is the most common bacterial infection in young infants, and the incidence of associated bacteremia has decreased in the recent decades. Host RNA expression signatures have shown great promise for distinguishing bacterial from viral infections in young infants. This prospective study included 121 young infants admitted to four pediatric emergency care departments in the capital region of Denmark due to symptoms of infection. We collected whole blood samples and performed differential gene expression analysis. Further, we tested the classification performance of a two-gene host RNA expression signature approaching clinical implementation. Several genes were differentially expressed between young infants with UTI without bacteremia and viral infection. However, limited immunological response was detected in UTI without bacteremia compared to a more pronounced response in viral infection. The performance of the two-gene signature was limited, especially in cases of UTI without bloodstream involvement. Our results indicate a need for further investigation and consideration of UTI in young infants before implementing host RNA expression signatures in clinical practice.
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Affiliation(s)
- Kia Hee Schultz Dungu
- Department of Pediatrics & Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark; (K.H.S.D.)
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Emma Louise Malchau Carlsen
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Neonatology, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Jonathan Peter Glenthøj
- Department of Pediatrics & Adolescent Medicine, Copenhagen University Hospital North Zealand, 3400 Hillerød, Denmark
| | - Lisbeth Samsø Schmidt
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Pediatrics & Adolescent Medicine, Copenhagen University Hospital Herlev, 2730 Herlev, Denmark
| | - Inger Merete Jørgensen
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Pediatrics & Adolescent Medicine, Copenhagen University Hospital North Zealand, 3400 Hillerød, Denmark
| | - Dina Cortes
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Pediatrics & Adolescent Medicine, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark
| | - Anja Poulsen
- Department of Pediatrics & Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark; (K.H.S.D.)
| | - Nadja Hawwa Vissing
- Department of Pediatrics & Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark; (K.H.S.D.)
| | - Frederik Otzen Bagger
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Ulrikka Nygaard
- Department of Pediatrics & Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark; (K.H.S.D.)
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
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15
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Dunican C, Andradi-Brown C, Ebmeier S, Georgiadou A, Cunnington AJ. The malarial blood transcriptome: translational applications. Biochem Soc Trans 2024; 52:651-660. [PMID: 38421063 PMCID: PMC11088907 DOI: 10.1042/bst20230497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
The blood transcriptome of malaria patients has been used extensively to elucidate the pathophysiological mechanisms and host immune responses to disease, identify candidate diagnostic and prognostic biomarkers, and reveal new therapeutic targets for drug discovery. This review gives a high-level overview of the three main translational applications of these studies (diagnostics, prognostics, and therapeutics) by summarising recent literature and outlining the main limitations and future directions of each application. It highlights the need for consistent and accurate definitions of disease states and subject groups and discusses how prognostic studies must distinguish clearly between analyses that attempt to predict future disease states and those which attempt to discriminate between current disease states (classification). Lastly it examines how many promising therapeutics fail due to the choice of imperfect animal models for pre-clinical testing and lack of appropriate validation studies in humans, and how future transcriptional studies may be utilised to overcome some of these limitations.
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Affiliation(s)
- Claire Dunican
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
| | - Clare Andradi-Brown
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
| | - Stefan Ebmeier
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
| | - Athina Georgiadou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
| | - Aubrey J. Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
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16
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Alonso-Rodríguez N, Vianello E, van Veen S, Jenum S, Tonby K, van Riessen R, Lai X, Mortensen R, Ottenhoff THM, Dyrhol-Riise AM. Whole blood RNA signatures in tuberculosis patients receiving H56:IC31 vaccine as adjunctive therapy. Front Immunol 2024; 15:1350593. [PMID: 38433842 PMCID: PMC10904528 DOI: 10.3389/fimmu.2024.1350593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/25/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction Therapeutic vaccination in tuberculosis (TB) represents a Host Directed Therapy strategy which enhances immune responses in order to improve clinical outcomes and shorten TB treatment. Previously, we have shown that the subunit H56:IC31 vaccine induced both humoral and cellular immune responses when administered to TB patients adjunctive to standard TB treatment (TBCOX2 study, NCT02503839). Here we present the longitudinal whole blood gene expression patterns in H56:IC31 vaccinated TB patients compared to controls receiving standard TB treatment only. Methods The H56:IC31 group (N=11) and Control group (N=7) underwent first-line TB treatment for 182 days. The H56:IC31 group received 5 micrograms of the H56:IC31 vaccine (Statens Serum Institut; SSI, Valneva Austria GmbH) intramuscularly at day 84 and day 140. Total RNA was extracted from whole blood samples collected in PAXgene tubes on days 0, 84, 98, 140, 154, 182 and 238. The expression level of 183 immune-related genes was measured by high-throughput microfluidic qPCR (Biomark HD system, Standard BioTools). Results The targeted gene expression profiling unveiled the upregulation of modules such as interferon (IFN) signalling genes, pattern recognition receptors and small nucleotide guanosine triphosphate (GTP)-ases in the vaccinated group compared to controls two weeks after administration of the first H56:IC31 vaccine. Additionally, the longitudinal analysis of the Adolescent Cohort Study-Correlation of Risk (ACS-COR) signature showed a progressive downregulation in both study arms towards the end of TB treatment, in congruence with reported treatment responses and clinical improvements. Still, two months after the end of TB treatment, vaccinated patients, and especially those developing both cellular and humoral vaccine responses, showed a lower expression of the ACS-COR genes compared to controls. Discussion Our data report gene expression patterns following H56:IC31 vaccination which might be interpreted as a lower risk of relapse in therapeutically vaccinated patients. Further studies are needed to conclude if these gene expression patterns could be used as prognostic biosignatures for therapeutic TB vaccine responses.
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Affiliation(s)
| | - Eleonora Vianello
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Suzanne van Veen
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Synne Jenum
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Kristian Tonby
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rosalie van Riessen
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Xiaoran Lai
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rasmus Mortensen
- Deptartment of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Anne Ma Dyrhol-Riise
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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17
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Drain PK, Dalmat RR. The elusive allure of a rapid host blood signature for tuberculosis disease. J Clin Microbiol 2024; 62:e0128923. [PMID: 38270458 PMCID: PMC10865849 DOI: 10.1128/jcm.01289-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
A rapid host transcriptional signature cartridge could be a major advancement for tuberculosis diagnosis and treatment monitoring. In a recent study, M. Li, Y. Qiu, M. Guo, R. Qu, et al. (J Clin Microbiol 61:e00911-23, 2023, https://doi.org/10.1128/jcm.00911-23) conducted an evaluation of the Cepheid 3-gene assay (Xpert-MTB-HR) within a diagnostic case-control study in China. While the study provides a strong contribution for determining the value of the Xpert-MTB-HR assay for diagnostic accuracy and treatment response, further assay optimization and more prospective studies are necessary before adaptation into clinical practice.
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Affiliation(s)
- Paul K. Drain
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ronit R. Dalmat
- Department of Global Health, University of Washington, Seattle, Washington, USA
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18
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Montaldo P, Burgod C, Herberg JA, Kaforou M, Cunnington AJ, Mejias A, Cirillo G, Miraglia Del Giudice E, Capristo C, Bandiya P, Kamalaratnam CN, Chandramohan R, Manerkar S, Rodrigo R, Sumanasena S, Krishnan V, Pant S, Shankaran S, Thayyil S. Whole-Blood Gene Expression Profile After Hypoxic-Ischemic Encephalopathy. JAMA Netw Open 2024; 7:e2354433. [PMID: 38306098 PMCID: PMC10837749 DOI: 10.1001/jamanetworkopen.2023.54433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/06/2023] [Indexed: 02/03/2024] Open
Abstract
Importance Induced hypothermia, the standard treatment for hypoxic-ischemic encephalopathy (HIE) in high-income countries (HICs), is less effective in the low-income populations in South Asia, who have the highest disease burden. Objective To investigate the differences in blood genome expression profiles of neonates with HIE from an HIC vs neonates with HIE from South Asia. Design, Setting, and Participants This case-control study analyzed data from (1) a prospective observational study involving neonates with moderate or severe HIE who underwent whole-body hypothermia between January 2017 and June 2019 and age-matched term healthy controls in Italy and (2) a randomized clinical trial involving neonates with moderate or severe HIE in India, Sri Lanka, and Bangladesh recruited between August 2015 and February 2019. Data were analyzed between October 2020 and August 2023. Exposure Whole-blood RNA that underwent next-generation sequencing. Main Outcome and Measures The primary outcomes were whole-blood genome expression profile at birth associated with adverse outcome (death or disability at 18 months) after HIE in the HIC and South Asia cohorts and changes in whole-genome expression profile during the first 72 hours after birth in neonates with HIE and healthy controls from the HIC cohort. Blood samples for RNA extraction were collected before whole-body hypothermia at 4 time points (6, 24, 48, and 72 hours after birth) for the HIC cohort. Only 1 blood sample was drawn within 6 hours after birth for the South Asia cohort. Results The HIC cohort was composed of 35 neonates (21 females [60.0%]) with a median (IQR) birth weight of 3.3 (3.0-3.6) kg and gestational age of 40.0 (39.0-40.6) weeks. The South Asia cohort consisted of 99 neonates (57 males [57.6%]) with a median (IQR) birth weight of 2.9 (2.7-3.3) kg and gestational age of 39.0 (38.0-40.0) weeks. Healthy controls included 14 neonates (9 females [64.3%]) with a median (IQR) birth weight of 3.4 (3.2-3.7) kg and gestational age of 39.2 (38.9-40.4) weeks. A total of 1793 significant genes in the HIC cohort and 99 significant genes in the South Asia cohort were associated with adverse outcome (false discovery rate <0.05). Only 11 of these genes were in common, and all had opposite direction in fold change. The most significant pathways associated with adverse outcome were downregulation of eukaryotic translation initiation factor 2 signaling in the HIC cohort (z score = -4.56; P < .001) and aldosterone signaling in epithelial cells in the South Asia cohort (z score = null; P < .001). The genome expression profile of neonates with HIE (n = 35) at birth, 24 hours, 48 hours, and 72 hours remained significantly different from that of age-matched healthy controls in the HIC cohort (n = 14). Conclusions and Relevance This case-control study found that disease mechanisms underlying HIE were primarily associated with acute hypoxia in the HIC cohort and nonacute hypoxia in the South Asia cohort. This finding might explain the lack of hypothermic neuroprotection.
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Affiliation(s)
- Paolo Montaldo
- Centre for Perinatal Neuroscience, Department of Brain Sciences, Imperial College London, London, United Kingdom
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Constance Burgod
- Centre for Perinatal Neuroscience, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Jethro A. Herberg
- Section of Paediatric Infectious Disease and Centre for Paediatrics and Child Health, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease and Centre for Paediatrics and Child Health, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Aubrey J. Cunnington
- Section of Paediatric Infectious Disease and Centre for Paediatrics and Child Health, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Asuncion Mejias
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio
| | - Grazia Cirillo
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Emanuele Miraglia Del Giudice
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Carlo Capristo
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Prathik Bandiya
- Department of Neonatology, Indira Gandhi Institute of Child Health, Bengaluru, India
| | | | - Rema Chandramohan
- Institute of Child Health, Department of Neonatology, Madras Medical College, Chennai, India
| | - Swati Manerkar
- Department of Neonatology, Lokmanya Tilak Municipal Medical College, Mumbai, India
| | - Ranmali Rodrigo
- Department of Pediatrics, University of Kelaniya, Colombo, Sri Lanka
| | | | - Vaisakh Krishnan
- Centre for Perinatal Neuroscience, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Stuti Pant
- Centre for Perinatal Neuroscience, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Seetha Shankaran
- Neonatal-Perinatal Medicine, Wayne State University, Detroit, Michigan
| | - Sudhin Thayyil
- Centre for Perinatal Neuroscience, Department of Brain Sciences, Imperial College London, London, United Kingdom
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Togun TO, Kampmann B. Diagnostics for childhood tuberculosis: a marathon rather than a sprint. THE LANCET. INFECTIOUS DISEASES 2024; 24:110-112. [PMID: 37918415 DOI: 10.1016/s1473-3099(23)00517-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 11/04/2023]
Affiliation(s)
- Toyin Omotayo Togun
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Beate Kampmann
- Charité Universitatsmedizin Berlin, Centre for Global Health and Institut für Internationale Gesundheit, Berlin 10117, Germany.
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20
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Olbrich L, Verghese VP, Franckling-Smith Z, Sabi I, Ntinginya NE, Mfinanga A, Banze D, Viegas S, Khosa C, Semphere R, Nliwasa M, McHugh TD, Larsson L, Razid A, Song R, Corbett EL, Nabeta P, Trollip A, Graham SM, Hoelscher M, Geldmacher C, Zar HJ, Michael JS, Heinrich N. Diagnostic accuracy of a three-gene Mycobacterium tuberculosis host response cartridge using fingerstick blood for childhood tuberculosis: a multicentre prospective study in low-income and middle-income countries. THE LANCET. INFECTIOUS DISEASES 2024; 24:140-149. [PMID: 37918414 PMCID: PMC10808504 DOI: 10.1016/s1473-3099(23)00491-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Childhood tuberculosis remains a major cause of morbidity and mortality in part due to missed diagnosis. Diagnostic methods with enhanced sensitivity using easy-to-obtain specimens are needed. We aimed to assess the diagnostic accuracy of the Cepheid Mycobacterium tuberculosis Host Response prototype cartridge (MTB-HR), a candidate test measuring a three-gene transcriptomic signature from fingerstick blood, in children with presumptive tuberculosis disease. METHODS RaPaed-TB was a prospective diagnostic accuracy study conducted at four sites in African countries (Malawi, Mozambique, South Africa, and Tanzania) and one site in India. Children younger than 15 years with presumptive pulmonary or extrapulmonary tuberculosis were enrolled between Jan 21, 2019, and June 30, 2021. MTB-HR was performed at baseline and at 1 month in all children and was repeated at 3 months and 6 months in children on tuberculosis treatment. Accuracy was compared with tuberculosis status based on standardised microbiological, radiological, and clinical data. FINDINGS 5313 potentially eligible children were screened, of whom 975 were eligible. 784 children had MTB-HR test results, of whom 639 had a diagnostic classification and were included in the analysis. MTB-HR differentiated children with culture-confirmed tuberculosis from those with unlikely tuberculosis with a sensitivity of 59·8% (95% CI 50·8-68·4). Using any microbiological confirmation (culture, Xpert MTB/RIF Ultra, or both), sensitivity was 41·6% (34·7-48·7), and using a composite clinical reference standard, sensitivity was 29·6% (25·4-34·2). Specificity for all three reference standards was 90·3% (95% CI 85·5-94·0). Performance was similar in different age groups and by malnutrition status. Among children living with HIV, accuracy against the strict reference standard tended to be lower (sensitivity 50·0%, 15·7-84·3) compared with those without HIV (61·0%, 51·6-69·9), although the difference did not reach statistical significance. Combining baseline MTB-HR result with one Ultra result identified 71·2% of children with microbiologically confirmed tuberculosis. INTERPRETATION MTB-HR showed promising diagnostic accuracy for culture-confirmed tuberculosis in this large, geographically diverse, paediatric cohort and hard-to-diagnose subgroups. FUNDING European and Developing Countries Clinical Trials Partnership, UK Medical Research Council, Swedish International Development Cooperation Agency, Bundesministerium für Bildung und Forschung; German Center for Infection Research (DZIF).
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Affiliation(s)
- Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Fraunhofer Institute ITMP, Immunology, Infection and Pandemic Research, Munich, Germany; Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Valsan P Verghese
- Pediatric Infectious Diseases, Department of Pediatrics, Christian Medical College, Vellore, India
| | - Zoe Franckling-Smith
- Department of Paediatrics and Child Health, SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Issa Sabi
- Mbeya Medical Research Centre, National Institute for Medical Research, Mbeya, Tanzania
| | - Nyanda E Ntinginya
- Mbeya Medical Research Centre, National Institute for Medical Research, Mbeya, Tanzania
| | - Alfred Mfinanga
- Mbeya Medical Research Centre, National Institute for Medical Research, Mbeya, Tanzania
| | - Denise Banze
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Sofia Viegas
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Celso Khosa
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Robina Semphere
- Helse Nord Tuberculosis Initiative, Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Marriott Nliwasa
- Helse Nord Tuberculosis Initiative, Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, UK
| | - Leyla Larsson
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Alia Razid
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Rinn Song
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Elizabeth L Corbett
- Helse Nord Tuberculosis Initiative, Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi; Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Pamela Nabeta
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Andre Trollip
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Stephen M Graham
- Department of Paediatrics, University of Melbourne and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; CIHLMU Center for International Health, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Fraunhofer Institute ITMP, Immunology, Infection and Pandemic Research, Munich, Germany; Unit Global Health, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Fraunhofer Institute ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
| | - Heather J Zar
- Department of Paediatrics and Child Health, SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | | | - Norbert Heinrich
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany; CIHLMU Center for International Health, LMU University Hospital, LMU Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Fraunhofer Institute ITMP, Immunology, Infection and Pandemic Research, Munich, Germany.
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21
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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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22
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Liu Y, Zhang L, Wu F, Liu Y, Li Y, Chen Y. Identification and validation of a pyroptosis-related signature in identifying active tuberculosis via a deep learning algorithm. Front Cell Infect Microbiol 2023; 13:1273140. [PMID: 38029270 PMCID: PMC10646574 DOI: 10.3389/fcimb.2023.1273140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Active tuberculosis (ATB), instigated by Mycobacterium tuberculosis (M.tb), rises as a primary instigator of morbidity and mortality within the realm of infectious illnesses. A significant portion of M.tb infections maintain an asymptomatic nature, recognizably termed as latent tuberculosis infections (LTBI). The complexities inherent to its diagnosis significantly hamper the initiatives aimed at its control and eventual eradication. Methodology Utilizing the Gene Expression Omnibus (GEO), we procured two dedicated microarray datasets, labeled GSE39940 and GSE37250. The technique of weighted correlation network analysis was employed to discern the co-expression modules from the differentially expressed genes derived from the first dataset, GSE39940. Consequently, a pyroptosis-related module was garnered, facilitating the identification of a pyroptosis-related signature (PRS) diagnostic model through the application of a neural network algorithm. With the aid of Single Sample Gene Set Enrichment Analysis (ssGSEA), we further examined the immune cells engaged in the pyroptosis process in the context of active ATB. Lastly, dataset GSE37250 played a crucial role as a validating cohort, aimed at evaluating the diagnostic prowess of our model. Results In executing the Weighted Gene Co-expression Network Analysis (WGCNA), a total of nine discrete co-expression modules were lucidly elucidated. Module 1 demonstrated a potent correlation with pyroptosis. A predictive diagnostic paradigm comprising three pyroptosis-related signatures, specifically AIM2, CASP8, and NAIP, was devised accordingly. The established PRS model exhibited outstanding accuracy across both cohorts, with the area under the curve (AUC) being respectively articulated as 0.946 and 0.787. Conclusion The present research succeeded in identifying the pyroptosis-related signature within the pathogenetic framework of ATB. Furthermore, we developed a diagnostic model which exuded a remarkable potential for efficient and accurate diagnosis.
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Affiliation(s)
- Yuchen Liu
- Division of Infectious Diseases, Department of Internal Medicine, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Epidemiology Unit, Peking Union Medical College, International Clinical Epidemiology Network, Beijing, China
- Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lifan Zhang
- Division of Infectious Diseases, Department of Internal Medicine, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Epidemiology Unit, Peking Union Medical College, International Clinical Epidemiology Network, Beijing, China
- Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fengying Wu
- Division of Infectious Diseases, Department of Internal Medicine, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Epidemiology Unit, Peking Union Medical College, International Clinical Epidemiology Network, Beijing, China
- Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ye Liu
- Division of Infectious Diseases, Department of Internal Medicine, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Epidemiology Unit, Peking Union Medical College, International Clinical Epidemiology Network, Beijing, China
- Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanchun Li
- Division of Infectious Diseases, Department of Internal Medicine, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Epidemiology Unit, Peking Union Medical College, International Clinical Epidemiology Network, Beijing, China
- Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Chen
- Division of Infectious Diseases, Department of Internal Medicine, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Epidemiology Unit, Peking Union Medical College, International Clinical Epidemiology Network, Beijing, China
- Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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23
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Shaikh A, Rodrigues C. What's New in the Molecular Diagnosis of Childhood Tuberculosis? Pediatr Infect Dis J 2023; 42:e377-e379. [PMID: 37463349 DOI: 10.1097/inf.0000000000004044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Affiliation(s)
- Ambreen Shaikh
- From the Department of Laboratory Medicine, Section Tuberculosis, Foundation Medical Research, Worli, Mumbai, India
| | - Camilla Rodrigues
- Department of Laboratory Medicine, Section Microbiology, Hinduja Hospital, Mahim, Mumbai, India
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24
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Gao Y, Sun F. Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies. PLoS Comput Biol 2023; 19:e1010608. [PMID: 37844077 PMCID: PMC10602384 DOI: 10.1371/journal.pcbi.1010608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2023] [Accepted: 09/30/2023] [Indexed: 10/18/2023] Open
Abstract
Heterogeneity in different genomic studies compromises the performance of machine learning models in cross-study phenotype predictions. Overcoming heterogeneity when incorporating different studies in terms of phenotype prediction is a challenging and critical step for developing machine learning algorithms with reproducible prediction performance on independent datasets. We investigated the best approaches to integrate different studies of the same type of omics data under a variety of different heterogeneities. We developed a comprehensive workflow to simulate a variety of different types of heterogeneity and evaluate the performances of different integration methods together with batch normalization by using ComBat. We also demonstrated the results through realistic applications on six colorectal cancer (CRC) metagenomic studies and six tuberculosis (TB) gene expression studies, respectively. We showed that heterogeneity in different genomic studies can markedly negatively impact the machine learning classifier's reproducibility. ComBat normalization improved the prediction performance of machine learning classifier when heterogeneous populations are present, and could successfully remove batch effects within the same population. We also showed that the machine learning classifier's prediction accuracy can be markedly decreased as the underlying disease model became more different in training and test populations. Comparing different merging and integration methods, we found that merging and integration methods can outperform each other in different scenarios. In the realistic applications, we observed that the prediction accuracy improved when applying ComBat normalization with merging or integration methods in both CRC and TB studies. We illustrated that batch normalization is essential for mitigating both population differences of different studies and batch effects. We also showed that both merging strategy and integration methods can achieve good performances when combined with batch normalization. In addition, we explored the potential of boosting phenotype prediction performance by rank aggregation methods and showed that rank aggregation methods had similar performance as other ensemble learning approaches.
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Affiliation(s)
- Yilin Gao
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
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25
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Habgood-Coote D, Wilson C, Shimizu C, Barendregt AM, Philipsen R, Galassini R, Calle IR, Workman L, Agyeman PKA, Ferwerda G, Anderson ST, van den Berg JM, Emonts M, Carrol ED, Fink CG, de Groot R, Hibberd ML, Kanegaye J, Nicol MP, Paulus S, Pollard AJ, Salas A, Secka F, Schlapbach LJ, Tremoulet AH, Walther M, Zenz W, Van der Flier M, Zar HJ, Kuijpers T, Burns JC, Martinón-Torres F, Wright VJ, Coin LJM, Cunnington AJ, Herberg JA, Levin M, Kaforou M. Diagnosis of childhood febrile illness using a multi-class blood RNA molecular signature. MED 2023; 4:635-654.e5. [PMID: 37597512 DOI: 10.1016/j.medj.2023.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Appropriate treatment and management of children presenting with fever depend on accurate and timely diagnosis, but current diagnostic tests lack sensitivity and specificity and are frequently too slow to inform initial treatment. As an alternative to pathogen detection, host gene expression signatures in blood have shown promise in discriminating several infectious and inflammatory diseases in a dichotomous manner. However, differential diagnosis requires simultaneous consideration of multiple diseases. Here, we show that diverse infectious and inflammatory diseases can be discriminated by the expression levels of a single panel of genes in blood. METHODS A multi-class supervised machine-learning approach, incorporating clinical consequence of misdiagnosis as a "cost" weighting, was applied to a whole-blood transcriptomic microarray dataset, incorporating 12 publicly available datasets, including 1,212 children with 18 infectious or inflammatory diseases. The transcriptional panel identified was further validated in a new RNA sequencing dataset comprising 411 febrile children. FINDINGS We identified 161 transcripts that classified patients into 18 disease categories, reflecting individual causative pathogen and specific disease, as well as reliable prediction of broad classes comprising bacterial infection, viral infection, malaria, tuberculosis, or inflammatory disease. The transcriptional panel was validated in an independent cohort and benchmarked against existing dichotomous RNA signatures. CONCLUSIONS Our data suggest that classification of febrile illness can be achieved with a single blood sample and opens the way for a new approach for clinical diagnosis. FUNDING European Union's Seventh Framework no. 279185; Horizon2020 no. 668303 PERFORM; Wellcome Trust (206508/Z/17/Z); Medical Research Foundation (MRF-160-0008-ELP-KAFO-C0801); NIHR Imperial BRC.
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Affiliation(s)
- Dominic Habgood-Coote
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Clare Wilson
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Chisato Shimizu
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Anouk M Barendregt
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Ria Philipsen
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Rachel Galassini
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Irene Rivero Calle
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Lesley Workman
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Philipp K A Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gerben Ferwerda
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Suzanne T Anderson
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - J Merlijn van den Berg
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Marieke Emonts
- Great North Children's Hospital, Department of Paediatric Immunology, Infectious Diseases & Allergy and NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Enitan D Carrol
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Colin G Fink
- Micropathology Ltd Research and Diagnosis, Coventry, UK; University of Warwick, Coventry, UK
| | - Ronald de Groot
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - John Kanegaye
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mark P Nicol
- Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Stéphane Paulus
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Antonio Salas
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Fatou Secka
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Luregn J Schlapbach
- Pediatric and Neonatal Intensive Care Unit, and Children`s Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Child Health Research Centre, The University of Queensland, and Paediatric Intensive Care Unit, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Adriana H Tremoulet
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Walther
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Werner Zenz
- University Clinic of Paediatrics and Adolescent Medicine, Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Michiel Van der Flier
- Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Paediatric Infectious Diseases and Immunology Amalia Children's Hospital, Radboudumc, Nijmegen, the Netherlands
| | - Heather J Zar
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands; Department of Blood Cell Research, Sanquin Blood Supply, Division Research and Landsteiner Laboratory of Amsterdam UMC (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Jane C Burns
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Federico Martinón-Torres
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Victoria J Wright
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Jethro A Herberg
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK.
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Li A, Bao J, Gao S, He Y, Nie X, Hosyanto FF, He X, Li T, Xu L. MicroRNA hsa-miR-320a-3p and Its Targeted mRNA FKBP5 Were Differentially Expressed in Patients with HIV/TB Co-Infection. ACS Infect Dis 2023; 9:1742-1753. [PMID: 37624586 DOI: 10.1021/acsinfecdis.3c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Among the PLWH (people living with HIV) population, the risk of developing active tuberculosis (TB) is increasing. Active TB also accelerates the deterioration of PLWH's immune function and is one of the leading causes of death in the PLWH population. So far, accurate diagnosis of active TB in the PLWH population remains challenging. Through data analysis of HIV/TB co-infection in the GEO database, the differentially expressed genes as well as their related microRNA (miRNA) were acquired and were further verified through clinical blood samples. Dual-luciferase assay was used to verify the mechanism of miRNA on mRNA. The enrichment of immune cells in database patient samples was analyzed by bioinformatics and finally verified by blood routine data. Our study found that FKBP5 (FK506 binding protein 5) was highly expressed in the HIV/TB co-infection group; hsa-miR-320a-3p was highly expressed in the HIV infection group but decreased in the HIV/TB co-infection group. Dual-luciferase assay results showed that hsa-miR-320a-3p mimics significantly reduced the relative luciferase activity of the WT-FKBP5 group; however, this phenomenon was not observed in the MUT-FKBP5 group. At the same time, as a key molecule of the immune-related pathway, FKBP5 is highly correlated with the amount of neutrophils, which provides a new suggestion for the treatment of the HIV/TB co-infection population. Our study found that hsa-miR-320a-3p can decrease FKBP5 expression, suggesting a potential regulatory role for FKBP5. The involvement of FKBP5 and its related molecule hsa-miR-320a-3p in HIV/TB co-infection proposes them as potential biomarkers for the diagnosis of active TB in the PLWH population.
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Affiliation(s)
- Anlong Li
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiajia Bao
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
- Hospital-Acquired Infection Control Department, First People's Hospital of Jintang County, Chengdu 610400, China
| | - Sijia Gao
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Ying He
- Central Laboratory, Chongqing Public Health Medical Center, Southwest University Public Health Hospital, Chongqing 400036, China
| | - Xiaoping Nie
- Central Laboratory, Chongqing Public Health Medical Center, Southwest University Public Health Hospital, Chongqing 400036, China
| | | | - Xintong He
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tongxin Li
- Central Laboratory, Chongqing Public Health Medical Center, Southwest University Public Health Hospital, Chongqing 400036, China
| | - Lei Xu
- Department of Pathogenic Biology, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
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27
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Bobak CA, Botha M, Workman L, Hill JE, Nicol MP, Holloway JW, Stein DJ, Martinez L, Zar HJ. Gene Expression in Cord Blood and Tuberculosis in Early Childhood: A Nested Case-Control Study in a South African Birth Cohort. Clin Infect Dis 2023; 77:438-449. [PMID: 37144357 PMCID: PMC10425199 DOI: 10.1093/cid/ciad268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 04/29/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Transcriptomic profiling of adults with tuberculosis (TB) has become increasingly common, predominantly for diagnostic and risk prediction purposes. However, few studies have evaluated signatures in children, particularly in identifying those at risk for developing TB disease. We investigated the relationship between gene expression obtained from umbilical cord blood and both tuberculin skin test conversion and incident TB disease through the first 5 years of life. METHODS We conducted a nested case-control study in the Drakenstein Child Health Study, a longitudinal, population-based birth cohort in South Africa. We applied transcriptome-wide screens to umbilical cord blood samples from neonates born to a subset of selected mothers (N = 131). Signatures identifying tuberculin conversion and risk of subsequent TB disease were identified from genome-wide analysis of RNA expression. RESULTS Gene expression signatures revealed clear differences predictive of tuberculin conversion (n = 26) and TB disease (n = 10); 114 genes were associated with tuberculin conversion and 30 genes were associated with the progression to TB disease among children with early infection. Coexpression network analysis revealed 6 modules associated with risk of TB infection or disease, including a module associated with neutrophil activation in immune response (P < .0001) and defense response to bacterium (P < .0001). CONCLUSIONS These findings suggest multiple detectable differences in gene expression at birth that were associated with risk of TB infection or disease throughout early childhood. Such measures may provide novel insights into TB pathogenesis and susceptibility.
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Affiliation(s)
- Carly A Bobak
- Department of Biomedical Data Science, Dartmouth College, Hanover, New Hampshire
| | - Maresa Botha
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
| | - Jane E Hill
- School of Biomedical Engineering and the School of Chemical and Biological Engineering, University of British Columbia, Vancouver, Canada
| | - Mark P Nicol
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Division of Medical Microbiology, University of Cape Town, South Africa
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton
- National Institute for Health and Care Research Southampton Biomedical Research Center, University Hospital Southampton, United Kingdom
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town
- Unit on Risk and Resilience in Mental Disorders, South African Medical Research Council
- Neuroscience Institute, University of Cape Town, South Africa
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Massachusetts
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
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28
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Suliman S, Jaganath D, DiNardo A. Predicting Pediatric Tuberculosis: The Need for Age-Specific Host Biosignatures. Clin Infect Dis 2023; 77:450-452. [PMID: 37144361 PMCID: PMC10425193 DOI: 10.1093/cid/ciad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/03/2023] [Indexed: 05/06/2023] Open
Affiliation(s)
- Sara Suliman
- Department of Medicine, Division of Experimental Medicine, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Devan Jaganath
- Division of Pediatric Infectious Diseases, University of California San Francisco, San Francisco, California, USA
| | - Andrew DiNardo
- Global TB Program, Center for Human Immunbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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29
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Vargas R, Abbott L, Bower D, Frahm N, Shaffer M, Yu WH. Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment. PLoS Comput Biol 2023; 19:e1010770. [PMID: 37471455 PMCID: PMC10393163 DOI: 10.1371/journal.pcbi.1010770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
While blood gene signatures have shown promise in tuberculosis (TB) diagnosis and treatment monitoring, most signatures derived from a single cohort may be insufficient to capture TB heterogeneity in populations and individuals. Here we report a new generalized approach combining a network-based meta-analysis with machine-learning modeling to leverage the power of heterogeneity among studies. The transcriptome datasets from 57 studies (37 TB and 20 viral infections) across demographics and TB disease states were used for gene signature discovery and model training and validation. The network-based meta-analysis identified a common 45-gene signature specific to active TB disease across studies. Two optimized random forest regression models, using the full or partial 45-gene signature, were then established to model the continuum from Mycobacterium tuberculosis infection to disease and treatment response. In model validation, using pooled multi-cohort datasets to mimic the real-world setting, the model provides robust predictive performance for incipient to active TB risk over a 2.5-year period with an AUROC of 0.85, 74.2% sensitivity, and 78.3% specificity, which approximates the minimum criteria (>75% sensitivity and >75% specificity) within the WHO target product profile for prediction of progression to TB. Moreover, the model strongly discriminates active TB from viral infection (AUROC 0.93, 95% CI 0.91-0.94). For treatment monitoring, the TB scores generated by the model statistically correlate with treatment responses over time and were predictive, even before treatment initiation, of standard treatment clinical outcomes. We demonstrate an end-to-end gene signature model development scheme that considers heterogeneity for TB risk estimation and treatment monitoring.
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Affiliation(s)
- Roger Vargas
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, United States of America
- Harvard University, Cambridge, Massachusetts, United States of America
| | - Liam Abbott
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, United States of America
| | - Daniel Bower
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, United States of America
| | - Nicole Frahm
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, United States of America
| | - Mike Shaffer
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, United States of America
| | - Wen-Han Yu
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, United States of America
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30
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Jackson HR, Miglietta L, Habgood-Coote D, D’Souza G, Shah P, Nichols S, Vito O, Powell O, Davidson MS, Shimizu C, Agyeman PKA, Beudeker CR, Brengel-Pesce K, Carrol ED, Carter MJ, De T, Eleftheriou I, Emonts M, Epalza C, Georgiou P, De Groot R, Fidler K, Fink C, van Keulen D, Kuijpers T, Moll H, Papatheodorou I, Paulus S, Pokorn M, Pollard AJ, Rivero-Calle I, Rojo P, Secka F, Schlapbach LJ, Tremoulet AH, Tsolia M, Usuf E, Van Der Flier M, Von Both U, Vermont C, Yeung S, Zavadska D, Zenz W, Coin LJM, Cunnington A, Burns JC, Wright V, Martinon-Torres F, Herberg JA, Rodriguez-Manzano J, Kaforou M, Levin M. Diagnosis of Multisystem Inflammatory Syndrome in Children by a Whole-Blood Transcriptional Signature. J Pediatric Infect Dis Soc 2023; 12:322-331. [PMID: 37255317 PMCID: PMC10312302 DOI: 10.1093/jpids/piad035] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/30/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki disease (KD), bacterial infections, and viral infections. METHODS Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020 and April 2021 were prospectively recruited. Whole-blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C (n = 38) to those from children with KD (n = 136), definite bacterial (DB; n = 188) and viral infections (DV; n = 138). Genes significantly differentially expressed (SDE) between MIS-C and comparator groups were identified. Feature selection was used to identify genes that optimally distinguish MIS-C from other diseases, which were subsequently translated into RT-qPCR assays and evaluated in an independent validation set comprising MIS-C (n = 37), KD (n = 19), DB (n = 56), DV (n = 43), and COVID-19 (n = 39). RESULTS In the discovery set, 5696 genes were SDE between MIS-C and combined comparator disease groups. Five genes were identified as potential MIS-C diagnostic biomarkers (HSPBAP1, VPS37C, TGFB1, MX2, and TRBV11-2), achieving an AUC of 96.8% (95% CI: 94.6%-98.9%) in the discovery set, and were translated into RT-qPCR assays. The RT-qPCR 5-gene signature achieved an AUC of 93.2% (95% CI: 88.3%-97.7%) in the independent validation set when distinguishing MIS-C from KD, DB, and DV. CONCLUSIONS MIS-C can be distinguished from KD, DB, and DV groups using a 5-gene blood RNA expression signature. The small number of genes in the signature and good performance in both discovery and validation sets should enable the development of a diagnostic test for MIS-C.
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Affiliation(s)
- Heather R Jackson
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Luca Miglietta
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Dominic Habgood-Coote
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Giselle D’Souza
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Priyen Shah
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Samuel Nichols
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Ortensia Vito
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Oliver Powell
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Maisey Salina Davidson
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Chisato Shimizu
- Department of Pediatrics, Rady Children’s Hospital and University of California San Diego, La Jolla, California, USA
| | - Philipp K A Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Coco R Beudeker
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children’s Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Karen Brengel-Pesce
- Joint Research Unit Hospices Civils de Lyon-bioMérieux, Lyon Sud Hospital, Pierre-Bénite, France
| | - Enitan D Carrol
- Department of Clinical Infection Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Michael J Carter
- Paediatric Intensive Care, Evelina London Children’s Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London, St Thomas’ Hospital, London, UK
| | - Tisham De
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Irini Eleftheriou
- Second Department of Paediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children’s Hospital, Athens, Greece
| | - Marieke Emonts
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Paediatric Infectious Diseases and Immunology Department, Newcastle upon Tyne Hospitals Foundation Trust, Great North Children’s Hospital, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle upon Tyne, UK
| | - Cristina Epalza
- Pediatric Infectious Diseases Unit, Pediatric Department, Hospital Doce de Octubre, Madrid, Spain
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Ronald De Groot
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology and Laboratory of Infectious Diseases, Radboud Institute of Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Katy Fidler
- Academic Department of Paediatrics, Royal Alexandra Children’s Hospital, University Hospitals Sussex, Brighton, UK
| | - Colin Fink
- Micropathology Ltd., University of Warwick, Warwick, UK
| | | | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Sanquin Research, Department of Blood Cell Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Henriette Moll
- Department of Pediatrics, Erasmus MC Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Irene Papatheodorou
- Gene Expression Team, European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Stephane Paulus
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Marko Pokorn
- Division of Pediatrics, University Medical Centre Ljubljana and Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Irene Rivero-Calle
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain
- Genetics–Vaccines–Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Pablo Rojo
- Pediatric Infectious Diseases Unit, Pediatric Department, Hospital Doce de Octubre, Madrid, Spain
| | - Fatou Secka
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Luregn J Schlapbach
- Department of Intensive Care and Neonatology, and Children’s Research Center, University Children`s Hospital Zurich, Zurich, Switzerland
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Adriana H Tremoulet
- Department of Pediatrics, Rady Children’s Hospital and University of California San Diego, La Jolla, California, USA
| | - Maria Tsolia
- Second Department of Paediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children’s Hospital, Athens, Greece
| | - Effua Usuf
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Michiel Van Der Flier
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children’s Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Ulrich Von Both
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Dr von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Clementien Vermont
- Department of Paediatric Infectious Diseases and Immunology, Erasmus MC Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Shunmay Yeung
- Clinical Research Department, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - Dace Zavadska
- Department of Pediatrics, Children’s Clinical University Hospital, Rīga, Latvia
| | - Werner Zenz
- Department of General Paediatrics, University Clinic of Paediatrics and Adolescent Medicine, Medical University Graz, Austria
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Aubrey Cunnington
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Jane C Burns
- Department of Pediatrics, Rady Children’s Hospital and University of California San Diego, La Jolla, California, USA
| | - Victoria Wright
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Federico Martinon-Torres
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain
- Genetics–Vaccines–Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Jethro A Herberg
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | | | - Myrsini Kaforou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
| | - Michael Levin
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, SW7 2AZ, UK
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Stein CM. Genetic epidemiology of resistance to M. tuberculosis Infection: importance of study design and recent findings. Genes Immun 2023; 24:117-123. [PMID: 37085579 PMCID: PMC10121418 DOI: 10.1038/s41435-023-00204-z] [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: 01/09/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 04/23/2023]
Abstract
Resistance to M. tuberculosis, often referred to as "RSTR" in the literature, is being increasingly studied because of its potential relevance as a clinical outcome in vaccine studies. This review starts by addressing the importance of epidemiological characterization of this phenotype, and ongoing challenges in that characterization. Then, this review summarizes the extant genetic and genomic studies of this phenotype, including heritability studies, candidate gene studies, and genome-wide association studies, as well as whole transcriptome studies. Findings from recent studies that used longitudinal characterization of the RSTR phenotype are compared to those using a cross-sectional definition, and the challenges of using tuberculin skin test and interferon-gamma release assay are discussed. Finally, future directions are proposed. Since this is a rapidly evolving area of public health significance, this review will help frame future research questions and study designs.
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Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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Olbrich L, Nliwasa M, Sabi I, Ntinginya NE, Khosa C, Banze D, Corbett EL, Semphere R, Verghese VP, Michael JS, Graham SM, Egere U, Schaaf HS, Morrison J, McHugh TD, Song R, Nabeta P, Trollip A, Geldmacher C, Hoelscher M, Zar HJ, Heinrich N. Rapid and Accurate Diagnosis of Pediatric Tuberculosis Disease: A Diagnostic Accuracy Study for Pediatric Tuberculosis. Pediatr Infect Dis J 2023; 42:353-360. [PMID: 36854097 PMCID: PMC10097493 DOI: 10.1097/inf.0000000000003853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2023] [Indexed: 03/02/2023]
Abstract
INTRODUCTION An estimated 1.2 million children develop tuberculosis (TB) every year with 240,000 dying because of missed diagnosis. Existing tools suffer from lack of accuracy and are often unavailable. Here, we describe the scientific and clinical methodology applied in RaPaed-TB, a diagnostic accuracy study. METHODS This prospective diagnostic accuracy study evaluating several candidate tests for TB was set out to recruit 1000 children <15 years with presumptive TB in 5 countries (Malawi, Mozambique, South Africa, Tanzania, India). Assessments at baseline included documentation of TB signs and symptoms, TB history, radiography, tuberculin skin test, HIV testing and spirometry. Respiratory samples for reference standard testing (culture, Xpert Ultra) included sputum (induced/spontaneous) or gastric aspirate, and nasopharyngeal aspirate (if <5 years). For novel tests, blood, urine and stool were collected. All participants were followed up at months 1 and 3, and month 6 if on TB treatment or unwell. The primary endpoint followed NIH-consensus statements on categorization of TB disease status for each participant. The study was approved by the sponsor's and all relevant local ethics committees. DISCUSSION As a diagnostic accuracy study for a disease with an imperfect reference standard, Rapid and Accurate Diagnosis of Pediatric Tuberculosis Disease (RaPaed-TB) was designed following a rigorous and complex methodology. This allows for the determination of diagnostic accuracy of novel assays and combination of testing strategies for optimal care for children, including high-risk groups (ie, very young, malnourished, children living with HIV). Being one of the largest of its kind, RaPaed-TB will inform the development of improved diagnostic approaches to increase case detection in pediatric TB.
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Affiliation(s)
- Laura Olbrich
- From the Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Oxford Vaccine Group, Department of Paediatrics, and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Marriott Nliwasa
- From the Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- Helse Nord Tuberculosis Initiative, Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Issa Sabi
- National Institute for Medical Research – Mbeya Medical Research Centre, Mbeya, Tanzania
- Centre for International Health, University Hospital, LMU Munich, Munich, Germany
| | - Nyanda E. Ntinginya
- National Institute for Medical Research – Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Celso Khosa
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Denise Banze
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Elizabeth L. Corbett
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Robina Semphere
- Helse Nord Tuberculosis Initiative, Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Valsan P. Verghese
- Pediatric Infectious Diseases, Department of Pediatrics, Christian Medical College (CMC), Vellore, India
| | - Joy Sarojini Michael
- Department of Clinical Microbiology, Christian Medical College (CMC), Vellore, India
| | - Stephen M. Graham
- Centre for International Child Health, University of Melbourne Department of Paediatrics, Royal Children’s Hospital, Melbourne, Australia
| | - Uzochukwu Egere
- Centre for International Health, University Hospital, LMU Munich, Munich, Germany
| | - H. Simon Schaaf
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Julie Morrison
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, Division of Infection & Immunity, University College, London, London, United Kingdom
| | - Rinn Song
- Oxford Vaccine Group, Department of Paediatrics, and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Pamela Nabeta
- FIND (Foundation for Innovative New Diagnostics), Geneva, Switzerland
| | - Andre Trollip
- FIND (Foundation for Innovative New Diagnostics), Geneva, Switzerland
| | - Christof Geldmacher
- From the Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Michael Hoelscher
- From the Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Centre for International Health, University Hospital, LMU Munich, Munich, Germany
| | - Heather J. Zar
- Department of Paediatrics & Child Health, SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Norbert Heinrich
- From the Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Centre for International Health, University Hospital, LMU Munich, Munich, Germany
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Lyu M, Zhou J, Zhou Y, Chong W, Xu W, Lai H, Niu L, Hai Y, Yao X, Gong S, Wang Q, Chen Y, Wang Y, Chen L, Zengwanggema, Zeng J, Wang C, Ying B. From tuberculosis bedside to bench: UBE2B splicing as a potential biomarker and its regulatory mechanism. Signal Transduct Target Ther 2023; 8:82. [PMID: 36828823 PMCID: PMC9958017 DOI: 10.1038/s41392-023-01346-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
Alternative splicing (AS) is an important approach for pathogens and hosts to remodel transcriptome. However, tuberculosis (TB)-related AS has not been sufficiently explored. Here we presented the first landscape of TB-related AS by long-read sequencing, and screened four AS events (S100A8-intron1-retention intron, RPS20-exon1-alternaitve promoter, KIF13B-exon4-skipping exon (SE) and UBE2B-exon7-SE) as potential biomarkers in an in-house cohort-1. The validations in an in-house cohort-2 (2274 samples) and public datasets (1557 samples) indicated that the latter three AS events are potential promising biomarkers for TB diagnosis, but not for TB progression and prognosis. The excellent performance of classifiers further underscored the diagnostic value of these three biomarkers. Subgroup analyses indicated that UBE2B-exon7-SE splicing was not affected by confounding factors and thus had relatively stable performance. The splicing of UBE2B-exon7-SE can be changed by heat-killed mycobacterium tuberculosis through inhibiting SRSF1 expression. After heat-killed mycobacterium tuberculosis stimulation, 231 ubiquitination proteins in macrophages were differentially expressed, and most of them are apoptosis-related proteins. Taken together, we depicted a global TB-associated splicing profile, developed TB-related AS biomarkers, demonstrated an optimal application scope of target biomarkers and preliminarily elucidated mycobacterium tuberculosis-host interaction from the perspective of splicing, offering a novel insight into the pathophysiology of TB.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jian Zhou
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weelic Chong
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, M5T 3M7, Canada
| | - Hongli Lai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lu Niu
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yang Hai
- Department of Radiology, Thomas Jefferson University Hospital, Philadelphia, PA, 19107, USA
| | - Xiaojun Yao
- Department of Thoracic Surgery, The Public and Health Clinic Centre of Chengdu, Chengdu, Sichuan, 610066, China
| | - Sheng Gong
- Department of Thoracic Surgery, The Public and Health Clinic Centre of Chengdu, Chengdu, Sichuan, 610066, China
| | - Qinglan Wang
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610213, China
| | - Yi Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Liyu Chen
- Department of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Zhaojue People's Hospital of Liangshan Prefecture, Liangshan Prefecture, Sichuan, 616150, China
| | - Zengwanggema
- Department of Laboratory Medicine, Ganzi People's Hospital, Ganzi Prefecture, Sichuan, 626099, China
| | - Jiongjiong Zeng
- Department of Laboratory Medicine, Ganzi People's Hospital, Ganzi Prefecture, Sichuan, 626099, China
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610213, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Mendelsohn SC, Verhage S, Mulenga H, Scriba TJ, Hatherill M. Systematic review of diagnostic and prognostic host blood transcriptomic signatures of tuberculosis disease in people living with HIV. Gates Open Res 2023; 7:27. [PMID: 37123047 PMCID: PMC10133453 DOI: 10.12688/gatesopenres.14327.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Background HIV-associated tuberculosis (TB) has high mortality; however, current triage and prognostic tools offer poor sensitivity and specificity, respectively. We conducted a systematic review of diagnostic and prognostic host-blood transcriptomic signatures of TB in people living with HIV (PLHIV). Methods We systematically searched online databases for studies published in English between 1990-2020. Eligible studies included PLHIV of any age in test or validation cohorts, and used microbiological or composite reference standards for TB diagnosis. Inclusion was not restricted by setting or participant age. Study selection, quality appraisal using the QUADAS-2 tool, and data extraction were conducted independently by two reviewers. Thereafter, narrative synthesis of included studies, and comparison of signatures performance, was performed. Results We screened 1,580 records and included 12 studies evaluating 31 host-blood transcriptomic signatures in 10 test or validation cohorts of PLHIV that differentiated individuals with TB from those with HIV alone, latent Mycobacterium tuberculosis infection, or other diseases (OD). Two (2/10; 20%) cohorts were prospective (29 TB cases; 51 OD) and 8 (80%) case-control (353 TB cases; 606 controls) design. All cohorts (10/10) were recruited in Sub-Saharan Africa and 9/10 (90%) had a high risk of bias. Ten signatures (10/31; 32%) met minimum WHO Target Product Profile (TPP) criteria for TB triage tests. Only one study (1/12; 8%) evaluated prognostic performance of a transcriptomic signature for progression to TB in PLHIV, which did not meet the minimum WHO prognostic TPP. Conclusions Generalisability of reported findings is limited by few studies enrolling PLHIV, limited geographical diversity, and predominantly case-control design, which also introduces spectrum bias. New prospective cohort studies are needed that include PLHIV and are conducted in diverse settings. Further research exploring the effect of HIV clinical, virological, and immunological factors on diagnostic performance is necessary for development and implementation of TB transcriptomic signatures in PLHIV.
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Affiliation(s)
- Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Savannah Verhage
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
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Wang X, VanValkenberg A, Odom-Mabey AR, Ellner JJ, Hochberg NS, Salgame P, Patil P, Johnson WE. Comparison of gene set scoring methods for reproducible evaluation of multiple tuberculosis gene signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.520627. [PMID: 36711818 PMCID: PMC9882404 DOI: 10.1101/2023.01.19.520627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rationale Many blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease, predict risk of progression from infection to disease, and monitor TB treatment outcomes. However, an unresolved issue is whether gene set enrichment analysis (GSEA) of the signature transcripts alone is sufficient for prediction and differentiation, or whether it is necessary to use the original statistical model created when the signature was derived. Intra-method comparison is complicated by the unavailability of original training data, missing details about the original trained model, and inadequate publicly-available software tools or source code implementing models. To facilitate these signatures' replicability and appropriate utilization in TB research, comprehensive comparisons between gene set scoring methods with cross-data validation of original model implementations are needed. Objectives We compared the performance of 19 TB gene signatures across 24 transcriptomic datasets using both re-rebuilt original models and gene set scoring methods to evaluate whether gene set scoring is a reasonable proxy to the performance of the original trained model. We have provided an open-access software implementation of the original models for all 19 signatures for future use. Methods We considered existing gene set scoring and machine learning methods, including ssGSEA, GSVA, PLAGE, Singscore, and Zscore, as alternative approaches to profile gene signature performance. The sample-size-weighted mean area under the curve (AUC) value was computed to measure each signature's performance across datasets. Correlation analysis and Wilcoxon paired tests were used to analyze the performance of enrichment methods with the original models. Measurement and Main Results For many signatures, the predictions from gene set scoring methods were highly correlated and statistically equivalent to the results given by the original diagnostic models. PLAGE outperformed all other gene scoring methods. In some cases, PLAGE outperformed the original models when considering signatures' weighted mean AUC values and the AUC results within individual studies. Conclusion Gene set enrichment scoring of existing blood-based biomarker gene sets can distinguish patients with active TB disease from latent TB infection and other clinical conditions with equivalent or improved accuracy compared to the original methods and models. These data justify using gene set scoring methods of published TB gene signatures for predicting TB risk and treatment outcomes, especially when original models are difficult to apply or implement.
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Affiliation(s)
- Xutao Wang
- Department of Biostatistics, Boston University, Boston, MA, USA
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Arthur VanValkenberg
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Aubrey R. Odom-Mabey
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Jerrold J. Ellner
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Natasha S. Hochberg
- Boston Medical Center, Boston, MA, USA
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, USA
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Prasad Patil
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - W. Evan Johnson
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, USA
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Ssekamatte P, Sande OJ, van Crevel R, Biraro IA. Immunologic, metabolic and genetic impact of diabetes on tuberculosis susceptibility. Front Immunol 2023; 14:1122255. [PMID: 36756113 PMCID: PMC9899803 DOI: 10.3389/fimmu.2023.1122255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023] Open
Abstract
Due to the increasing prevalence of diabetes mellitus (DM) globally, the interaction between DM and major global diseases like tuberculosis (TB) is of great public health significance, with evidence of DM having about a three-fold risk for TB disease. TB defense may be impacted by diabetes-related effects on immunity, metabolism, and gene transcription. An update on the epidemiological aspects of DM and TB, and the recent trends in understanding the DM-associated immunologic, metabolic, and genetic mechanisms of susceptibility to TB will be discussed in this review. This review highlights gaps in the incomplete understanding of the mechanisms that may relate to TB susceptibility in type 2 DM (T2DM). Understanding these three main domains regarding mechanisms of TB susceptibility in T2DM patients can help us build practical treatment plans to lessen the combined burden of the diseases in rampant areas.
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Affiliation(s)
- Phillip Ssekamatte
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Obondo James Sande
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Irene Andia Biraro
- Department of Internal Medicine, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
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Mendelsohn SC, Verhage S, Mulenga H, Scriba TJ, Hatherill M. Systematic review of diagnostic and prognostic host blood transcriptomic signatures of tuberculosis disease in people living with HIV. Gates Open Res 2023; 7:27. [PMID: 37123047 PMCID: PMC10133453.2 DOI: 10.12688/gatesopenres.14327.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 05/09/2023] Open
Abstract
Background HIV-associated tuberculosis (TB) has high mortality; however, current triage and prognostic tools offer poor sensitivity and specificity, respectively. We conducted a systematic review of diagnostic and prognostic host-blood transcriptomic signatures of TB in people living with HIV (PLHIV). Methods We systematically searched online databases for studies published in English between 1990-2020. Eligible studies included PLHIV of any age in test or validation cohorts, and used microbiological or composite reference standards for TB diagnosis. Inclusion was not restricted by setting or participant age. Study selection, quality appraisal using the QUADAS-2 tool, and data extraction were conducted independently by two reviewers. Thereafter, narrative synthesis of included studies, and comparison of signatures performance, was performed. Results We screened 1,580 records and included 12 studies evaluating 31 host-blood transcriptomic signatures in 10 test or validation cohorts of PLHIV that differentiated individuals with TB from those with HIV alone, latent Mycobacterium tuberculosis infection, or other diseases (OD). Two (2/10; 20%) cohorts were prospective (29 TB cases; 51 OD) and 8 (80%) case-control (353 TB cases; 606 controls) design. All cohorts (10/10) were recruited in Sub-Saharan Africa and 9/10 (90%) had a high risk of bias. Ten signatures (10/31; 32%) met minimum WHO Target Product Profile (TPP) criteria for TB triage tests. Only one study (1/12; 8%) evaluated prognostic performance of a transcriptomic signature for progression to TB in PLHIV, which did not meet the minimum WHO prognostic TPP. Conclusions Generalisability of reported findings is limited by few studies enrolling PLHIV, limited geographical diversity, and predominantly case-control design, which also introduces spectrum bias. New prospective cohort studies are needed that include PLHIV and are conducted in diverse settings. Further research exploring the effect of HIV clinical, virological, and immunological factors on diagnostic performance is necessary for development and implementation of TB transcriptomic signatures in PLHIV.
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Affiliation(s)
- Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Savannah Verhage
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
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Chendi BH, Jooste T, Scriba TJ, Kidd M, Mendelsohn S, Tonby K, Walzl G, Dyrhol-Riise AM, Chegou NN. Utility of a three-gene transcriptomic signature in the diagnosis of tuberculosis in a low-endemic hospital setting. Infect Dis (Lond) 2023; 55:44-54. [PMID: 36214761 DOI: 10.1080/23744235.2022.2129779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Host transcriptomic blood signatures have demonstrated diagnostic potential for tuberculosis (TB), requiring further validation across different geographical settings. Discriminating TB from other diseases with similar clinical manifestations is crucial for the development of an accurate immunodiagnostic tool. In this exploratory cohort study, we evaluated the performance of potential blood-based transcriptomic signatures in distinguishing TB disease from non-TB lower respiratory tract infections in hospitalised patients in a TB low-endemic country. METHOD Quantitative real-time polymerase chain reaction qPCR) was used to evaluate 26 previously published genes in blood from 31 patients (14 TB and 17 lower respiratory tract infection cases) admitted to Oslo University Hospital in Norway. The diagnostic accuracies of differentially expressed genes were determined by receiver operating characteristic curves. RESULTS A significant difference (p < .01) in the age distribution was observed between patients with TB (mean age, 40 ± 15 years) and lower respiratory tract infection (mean age 59 ± 12 years). Following adjustment for age, ETV7, GBP1, GBP5, P2RY14 and BLK were significantly differentially expressed between patients with TB and those with LRI. A general discriminant analysis generated a three-gene signature (BAFT2, ETV7 and CD1C), which diagnosed TB with an area under the receiver operating characteristic curve (AUC) of 0.86 (95% CI, 0.69 - 1.00), sensitivity of 69.23% (95% CI, 38.57%-90.91%) and specificity of 94.12% (95% CI, 71.31%-99.85%). CONCLUSION The three-genes signature may have potential to improve diagnosis of TB in a hospitalised low-burden setting. However, the influence of confounding variables or covariates such as age requires further evaluation in larger studies.
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Affiliation(s)
- Bih Hycenta Chendi
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tracey Jooste
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Thomas Jens Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Martin Kidd
- Department of Statistics and Actuarial Sciences, Centre for Statistical Consultation, Stellenbosch University, Cape Town, South Africa
| | - Simon Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Kristian Tonby
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anne M Dyrhol-Riise
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Novel Njweipi Chegou
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Wang J, Li Y, Wang N, Wu J, Ye X, Jiang Y, Tang L. Functions of exosomal non-coding RNAs to the infection with Mycobacterium tuberculosis. Front Immunol 2023; 14:1127214. [PMID: 37033928 PMCID: PMC10073540 DOI: 10.3389/fimmu.2023.1127214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Tuberculosis (TB) is a major infectious disease induced by Mycobacterium tuberculosis (M. tb) which causes the world's dominant fatal bacterial contagious disease. Increasing studies have indicated that exosomes may be a novel option for the diagnosis and treatment of TB. Exosomes are nanovesicles (30-150 nm) containing lipids, proteins and non-coding RNAs (ncRNAs) released from various cells, and can transfer their cargos and communicate between cells. Furthermore, exosomal ncRNAs exhibit diagnosis potential in bacterial infections, including TB. Additionally, differential exosomal ncRNAs regulate the physiological and pathological functions of M. tb-infected cells and act as diagnostic markers for TB. This current review explored the potential biological roles and the diagnostic application prospects of exosomal ncRNAs, and included recent information on their pathogenic and therapeutic functions in TB.
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Affiliation(s)
- Jianjun Wang
- Department of Clinical Laboratory, The First People’s Hospital of Kunshan, Suzhou, China
- *Correspondence: Lijun Tang, ; Jianjun Wang,
| | - Yujie Li
- Department of Clinical Laboratory, The First People’s Hospital of Kunshan, Suzhou, China
| | - Nan Wang
- Department of Clinical Laboratory, The First People’s Hospital of Kunshan, Suzhou, China
| | - Jianhong Wu
- Department of Clinical Laboratory, The First People’s Hospital of Kunshan, Suzhou, China
| | - Xiaojian Ye
- Department of Clinical Laboratory, The First People’s Hospital of Kunshan, Suzhou, China
| | - Yibiao Jiang
- Department of Clinical Laboratory, The First People’s Hospital of Kunshan, Suzhou, China
| | - Lijun Tang
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, China
- *Correspondence: Lijun Tang, ; Jianjun Wang,
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Yang BF, Zhai F, Yu S, An HJ, Cao ZH, Liu YH, Wang R, Cheng XX. Evaluation of IFIT3 and ORM1 as Biomarkers for Discriminating Active Tuberculosis from Latent Infection. Curr Med Sci 2022; 42:1201-1212. [PMID: 36462134 DOI: 10.1007/s11596-022-2649-6] [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: 08/09/2021] [Accepted: 11/16/2021] [Indexed: 12/04/2022]
Abstract
OBJECTIVE Current commercially available immunological tests cannot be used for discriminating active tuberculosis (TB) from latent TB infection. To evaluate the value of biomarker candidates in the diagnosis of active TB, this study aimed to identify differentially expressed genes in peripheral blood mononuclear cells (PBMCs) between patients with active TB and individuals with latent TB infection by transcriptome sequencing. METHODS The differentially expressed genes in unstimulated PBMCs and in Mycobacterium tuberculosis (Mtb) antigen-stimulated PBMCs from patients with active TB and individuals with latent TB infection were identified by transcriptome sequencing. Selected candidate genes were evaluated in cohorts consisting of 110 patients with TB, 30 individuals with latent TB infections, and 50 healthy controls by quantitative real-time RT-PCR. Receiver operating characteristic (ROC) curve analysis was performed to calculate the diagnostic value of the biomarker candidates. RESULTS Among the differentially expressed genes in PBMCs without Mtb antigen stimulation, interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) had the highest area under curve (AUC) value (0.918, 95% CI: 0.852-0.984, P<0.0001) in discriminating patients with active TB from individuals with latent TB infection, with a sensitivity of 91.86% and a specificity of 84.00%. In Mtb antigen-stimulated PBMCs, orosomucoid 1 (ORM1) had a high AUC value (0.833, 95% CI: 0.752-0.915, P<0.0001), with a sensitivity of 81.94% and a specificity of 70.00%. CONCLUSION IFIT3 and ORM1 might be potential biomarkers for discriminating active TB from latent TB infection.
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Affiliation(s)
- Bing-Fen Yang
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Senior Department of Tuberculosis, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Fei Zhai
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Senior Department of Tuberculosis, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Shan Yu
- Fourth Division, Senior Department of Tuberculosis, the Eighth Medical Center of PLA General Hospital, Beijing, 100091, China
| | - Hong-Juan An
- Department of Tuberculosis Prevention and Control, Senior Department of Tuberculosis, the Eighth Medical Center of PLA General Hospital, Beijing, 100091, China
| | - Zhi-Hong Cao
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Senior Department of Tuberculosis, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Yan-Hua Liu
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Senior Department of Tuberculosis, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Ruo Wang
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Senior Department of Tuberculosis, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Xiao-Xing Cheng
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Senior Department of Tuberculosis, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, 100091, China.
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Tripathi D, Devalraju KP, Neela VSK, Mukherjee T, Paidipally P, Radhakrishnan RK, Dozmorov I, Vankayalapati A, Ansari MS, Mallidi V, Bogam AK, Singh KP, Samten B, Valluri VL, Vankayalapati R. Metabolites enhance innate resistance to human Mycobacterium tuberculosis infection. JCI Insight 2022; 7:152357. [PMID: 36509283 DOI: 10.1172/jci.insight.152357] [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: 06/21/2021] [Accepted: 09/29/2022] [Indexed: 11/22/2022] Open
Abstract
To determine the mechanisms that mediate resistance to Mycobacterium tuberculosis (M. tuberculosis) infection in household contacts (HHCs) of patients with tuberculosis (TB), we followed 452 latent TB infection-negative (LTBI-) HHCs for 2 years. Those who remained LTBI- throughout the study were identified as nonconverters. At baseline, nonconverters had a higher percentage of CD14+ and CD3-CD56+CD27+CCR7+ memory-like natural killer (NK) cells. Using a whole-transcriptome and metabolomic approach, we identified deoxycorticosterone acetate as a metabolite with elevated concentrations in the plasma of nonconverters, and further studies showed that this metabolite enhanced glycolytic ATP flux in macrophages and restricted M. tuberculosis growth by enhancing antimicrobial peptide production through the expression of the surface receptor sialic acid binding Ig-like lectin-14. Another metabolite, 4-hydroxypyridine, from the plasma of nonconverters significantly enhanced the expansion of memory-like NK cells. Our findings demonstrate that increased levels of specific metabolites can regulate innate resistance against M. tuberculosis infection in HHCs of patients with TB who never develop LTBI or active TB.
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Affiliation(s)
- Deepak Tripathi
- Department of Pulmonary Immunology and Center for Biomedical Research, School of Community and Rural Health, University of Texas Health Science Center, Tyler, Texas, USA
| | | | | | - Tanmoy Mukherjee
- Department of Pulmonary Immunology and Center for Biomedical Research, School of Community and Rural Health, University of Texas Health Science Center, Tyler, Texas, USA
| | - Padmaja Paidipally
- Department of Pulmonary Immunology and Center for Biomedical Research, School of Community and Rural Health, University of Texas Health Science Center, Tyler, Texas, USA
| | - Rajesh Kumar Radhakrishnan
- Department of Pulmonary Immunology and Center for Biomedical Research, School of Community and Rural Health, University of Texas Health Science Center, Tyler, Texas, USA
| | - Igor Dozmorov
- Department of Immunology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Abhinav Vankayalapati
- Department of Pulmonary Immunology and Center for Biomedical Research, School of Community and Rural Health, University of Texas Health Science Center, Tyler, Texas, USA
| | - Mohammad Soheb Ansari
- Immunology and Molecular Biology Department, Bhagwan Mahavir Medical Research Centre, Hyderabad, India
| | - Varalakshmi Mallidi
- Immunology and Molecular Biology Department, Bhagwan Mahavir Medical Research Centre, Hyderabad, India
| | - Anvesh Kumar Bogam
- Immunology and Molecular Biology Department, Bhagwan Mahavir Medical Research Centre, Hyderabad, India
| | - Karan P Singh
- Department of Epidemiology and Biostatistics, School of Community and Rural Health, University of Texas Health Science Center, Tyler, Texas, USA
| | - Buka Samten
- Department of Pulmonary Immunology and Center for Biomedical Research, School of Community and Rural Health, University of Texas Health Science Center, Tyler, Texas, USA
| | - Vijaya Lakshmi Valluri
- Immunology and Molecular Biology Department, Bhagwan Mahavir Medical Research Centre, Hyderabad, India
| | - Ramakrishna Vankayalapati
- Department of Pulmonary Immunology and Center for Biomedical Research, School of Community and Rural Health, University of Texas Health Science Center, Tyler, Texas, USA
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42
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Taye K, Tolesa N, Tadewos A, Ketema W. Patterns of Childhood Tuberculosis Diagnosis in Hawassa University Comprehensive Specialized Hospital, Hawassa, Sidama Regional State, Ethiopia. Pediatric Health Med Ther 2022; 13:349-359. [PMID: 36386042 PMCID: PMC9657258 DOI: 10.2147/phmt.s380092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Because of the pauci bacillary nature of childhood tuberculosis and the difficulties in obtaining proper sputum samples from young children, diagnosing childhood tuberculosis (TB) is difficult. Childhood TB needs early identification and care since it advances swiftly to more advanced stages. This study was aimed to determine the patterns of all forms of childhood tuberculosis diagnosis at Hawassa University Comprehensive Specialized Hospital in Hawassa, Ethiopia. Methods A retrospective cross-sectional study was conducted from February 1, 2017 to January 30, 2021 among 175 children diagnosed and treated for tuberculosis in the pediatric ward. Children medical charts and pediatrics ward logbook were used to extract pertinent data by structured checklists. SPSS version 23.0 was used for data entry and statistical analysis. Results Of 175 children, fever was the leading clinical symptoms and diagnosed in 166 (94.9%) children followed by weight loss (154, 88%), and cough (136, 77.7%). In twenty seven out of 88 (30.6%) children, gastric aspirate was positive for TB infection by Xpert MTB/Rif, while 3/40 (7.5%) were positive for TB using fine needle aspiration cytology (FNAC), 19/66 (28.8%) had suggestive TB by cerebrospinal fluid analysis (CSF), 10/29 (34.5%) were smear positive for TB and 70/162 (43.2%) were suspected for TB by chest X-ray. Conclusion Despite recent breakthroughs in quick microbiological detection, such as Xpert MTB/Rif, this study revealed that more than half of the children, 89/175 (51%), were treated for TB diseases solely based on clinical criteria. This will significantly underestimate the true nature of the illness or disease and make them vulnerable to mistreatment. As a result, in order to appropriately treat the disease and manage patients in our settings, getting a microbiological diagnosis of childhood tuberculosis requires improvement, and we call for expanded availability and use of a more sensitive and specific diagnostic technique to circumvent these concerns.
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Affiliation(s)
- Kefyalew Taye
- Department of Pediatrics and Child Health, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
| | - Nagasa Tolesa
- Department of Pediatrics and Child Health, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
- Department of Pediatrics and Child Health, College of Medicine and Health Sciences, Dembi Dollo University, Dembi Dollo, Ethiopia
| | - Agete Tadewos
- School of Medical Laboratory Science, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
| | - Worku Ketema
- Department of Pediatrics and Child Health, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
- Correspondence: Worku Ketema, Department of Pediatrics and Child Health, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia, Email
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43
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Nogueira BMF, Krishnan S, Barreto‐Duarte B, Araújo‐Pereira M, Queiroz ATL, Ellner JJ, Salgame P, Scriba TJ, Sterling TR, Gupta A, Andrade BB. Diagnostic biomarkers for active tuberculosis: progress and challenges. EMBO Mol Med 2022; 14:e14088. [PMID: 36314872 PMCID: PMC9728055 DOI: 10.15252/emmm.202114088] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is a leading cause of morbidity and mortality from a single infectious agent, despite being preventable and curable. Early and accurate diagnosis of active TB is critical to both enhance patient care, improve patient outcomes, and break Mycobacterium tuberculosis (Mtb) transmission cycles. In 2020 an estimated 9.9 million people fell ill from Mtb, but only a little over half (5.8 million) received an active TB diagnosis and treatment. The World Health Organization has proposed target product profiles for biomarker- or biosignature-based diagnostics using point-of-care tests from easily accessible specimens such as urine or blood. Here we review and summarize progress made in the development of pathogen- and host-based biomarkers for active TB diagnosis. We describe several unique patient populations that have posed challenges to development of a universal diagnostic TB biomarker, such as people living with HIV, extrapulmonary TB, and children. We also review additional limitations to widespread validation and utilization of published biomarkers. We conclude with proposed solutions to enhance TB diagnostic biomarker validation and uptake.
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Affiliation(s)
- Betânia M F Nogueira
- Programa de Pós‐graduação em Ciências da SaúdeUniversidade Federal da BahiaSalvadorBrazil,Instituto Couto MaiaSalvadorBrazil,Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil
| | - Sonya Krishnan
- Division of Infectious Diseases, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Beatriz Barreto‐Duarte
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Curso de MedicinaUniversidade Salvador (UNIFACS)SalvadorBrazil,Programa de Pós‐Graduação em Clínica MédicaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil
| | - Mariana Araújo‐Pereira
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil,Faculdade de MedicinaUniversidade Federal da BahiaSalvadorBrazil
| | - Artur T L Queiroz
- Instituto Couto MaiaSalvadorBrazil,Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil
| | - Jerrold J Ellner
- Department of Medicine, Centre for Emerging PathogensRutgers‐New Jersey Medical SchoolNewarkNJUSA
| | - Padmini Salgame
- Department of Medicine, Centre for Emerging PathogensRutgers‐New Jersey Medical SchoolNewarkNJUSA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of PathologyUniversity of Cape TownCape TownSouth Africa
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Amita Gupta
- Division of Infectious Diseases, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Bruno B Andrade
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Curso de MedicinaUniversidade Salvador (UNIFACS)SalvadorBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil,Faculdade de MedicinaUniversidade Federal da BahiaSalvadorBrazil,Curso de MedicinaFaculdade de Tecnologia e Ciências (FTC)SalvadorBrazil,Curso de MedicinaEscola Bahiana de Medicina e Saúde Pública (EBMSP)SalvadorBrazil
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Abstract
The current diagnostic abilities for the detection of pediatric tuberculosis are suboptimal. Multiple factors contribute to the under-diagnosis of intrathoracic tuberculosis in children, namely the absence of pathognomonic features of the disease, low bacillary loads in respiratory specimens, challenges in sample collection, and inadequate access to diagnostic tools in high-burden settings. Nonetheless, the 2020s have witnessed encouraging progress in the area of novel diagnostics. Recent WHO-endorsed rapid molecular assays hold promise for use in service decentralization strategies, and new policy recommendations include stools as an alternative, child-friendly specimen for testing with the GeneXpert assay. The pipeline of promising assays in mid/late-stage development is expanding, and novel pediatric candidate biomarkers based on the host immune response are being identified for use in diagnostic and triage tests. For a new test to meet the pediatric target product profiles prioritized by the WHO, it is key that the peculiarities and needs of the hard-to-reach pediatric population are considered in the early planning phases of discovery, validation, and implementation studies.
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Affiliation(s)
| | - Pamela Nabeta
- FIND, the global alliance for diagnostics, Chemin des Mines 9, 1202 Geneva, Switzerland
| | - Morten Ruhwald
- FIND, the global alliance for diagnostics, Chemin des Mines 9, 1202 Geneva, Switzerland
| | - Rinn Song
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
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45
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Transcriptional Biomarkers for Treatment Monitoring of Pulmonary Drug-Resistant Tuberculosis: Protocol for a Prospective Observational Study in Indonesia. Trop Med Infect Dis 2022; 7:tropicalmed7110326. [DOI: 10.3390/tropicalmed7110326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022] Open
Abstract
Many blood-based gene expression biomarkers for monitoring tuberculosis (TB) treatment have been suggested so far, but promising biomarker results for drug-resistant TB treatment response have not been studied. This protocol presents a prospective observational study in Indonesia to profile the human blood transcriptome for predicting the response to drug-resistant TB treatment, focusing on pulmonary TB, and to adapt the specific RNA signature to the qRT-PCR platform. Longitudinal blood samples will be collected from 44 subjects with rifampicin resistant TB, confirmed by Xpert MTB/RIF, and 52 healthy controls. RNA-Seq will be performed to identify changes in the transcriptome following TB treatment. A discriminative RNA signature will be chosen and translated into a score for use in a quantitative PCR-based assay. This study will provide crucial information to guide the discovery and design of a clinically implementable tool to monitor the response of TB treatment.
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46
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Zhong X, Lei S, Lin JW, Ren M, Shu M. Aberrant expression of long non-coding RNAs in peripheral blood mononuclear cells response to tuberculosis in children. Medicine (Baltimore) 2022; 101:e31065. [PMID: 36281118 PMCID: PMC9592404 DOI: 10.1097/md.0000000000031065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We aimed to identify long non-coding RNAs (lncRNAs) aberrantly expressed in peripheral blood mononuclear cells (PBMCs) triggered by active tuberculosis (ATB), latent tuberculosis infection (LTBI), and healthy controls (HC). We examined lncRNAs expression in PBMCs isolated from children with ATB and LTBI, and from HC using RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to explore the biological processes and signaling pathways of aberrantly expressed mRNAs. A total of 348 and 205 lncRNAs were differentially expressed in the ATB and LTBI groups, respectively, compared to the HC group. Compared to the LTBI group, 125 lncRNAs were differentially expressed in the ATB group. Compared to the HC group, 2317 mRNAs were differentially expressed in the ATB group, and 1093 mRNAs were differentially expressed in the LTBI group. Compared to the LTBI group, 2328 mRNAs were differentially expressed in the ATB group. The upregulated mRNAs were mainly enriched in neutrophil activation, neutrophil-mediated biological processes, and positive regulation of immune response in tuberculosis (TB), whereas the downregulated mRNAs were enriched in signaling pathways and structural processes, such as the Wnt signaling pathway and rDNA heterochromatin assembly. This is the first study on the differential expression of lncRNAs in PBMCs of children with TB. We identified significant differences in the expression profiles of lncRNAs and mRNAs in the PBMCs of children with ATB, LTBI, and HC, which has important implications for exploring lncRNAs as novel biomarkers for the diagnosis of TB. In addition, further experimental identification and validation of lncRNA roles could help elucidate the underlying mechanisms of Mycobacterium tuberculosis infection in children.
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Affiliation(s)
- Xiaoling Zhong
- West China Second Hospital, Sichuan University/ Key Laboratory of Birth Defects and Related Diseases of Women and Children,Sichuan University, Ministry of Education, Chengdu, PR China
- The Third People’s Hospital of Chengdu/The Affiliated Hospital of Southwest Jiaotong University, Chengdu, PR China
| | - Shikun Lei
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, PR China
| | - Jing-Wen Lin
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, PR China
| | - Min Ren
- West China Second Hospital, Sichuan University/ Key Laboratory of Birth Defects and Related Diseases of Women and Children,Sichuan University, Ministry of Education, Chengdu, PR China
| | - Min Shu
- West China Second Hospital, Sichuan University/ Key Laboratory of Birth Defects and Related Diseases of Women and Children,Sichuan University, Ministry of Education, Chengdu, PR China
- West China Xiamen Hospital, Sichuan University, Xiamen, PR China
- * Correspondence: Min Shu, West China Second Hospital, Sichuan University/ Key Laboratory of Birth Defects and Related Diseases of Women and Children,Sichuan University, Ministry of Education, Chengdu 610041, PR China (e-mail: )
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47
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Bachanová P, Cheyne A, Broderick C, Newton SM, Levin M, Kaforou M. Comparative transcriptomic analysis of whole blood mycobacterial growth assays and tuberculosis patients' blood RNA profiles. Sci Rep 2022; 12:17684. [PMID: 36271270 PMCID: PMC9587058 DOI: 10.1038/s41598-022-20409-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/13/2022] [Indexed: 01/18/2023] Open
Abstract
In vitro whole blood infection models are used for elucidating the immune response to Mycobacterium tuberculosis (Mtb). They exhibit commonalities but also differences, to the in vivo blood transcriptional response during natural human Mtb disease. Here, we present a description of concordant and discordant components of the immune response in blood, quantified through transcriptional profiling in an in vitro whole blood infection model compared to whole blood from patients with tuberculosis disease. We identified concordantly and discordantly expressed gene modules and performed in silico cell deconvolution. A high degree of concordance of gene expression between both adult and paediatric in vivo-in vitro tuberculosis infection was identified. Concordance in paediatric in vivo vs in vitro comparison is largely characterised by immune suppression, while in adults the comparison is marked by concordant immune activation, particularly that of inflammation, chemokine, and interferon signalling. Discordance between in vitro and in vivo increases over time and is driven by T-cell regulation and monocyte-related gene expression, likely due to apoptotic depletion of monocytes and increasing relative fraction of longer-lived cell types, such as T and B cells. Our approach facilitates a more informed use of the whole blood in vitro model, while also accounting for its limitations.
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Affiliation(s)
- Petra Bachanová
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ashleigh Cheyne
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Claire Broderick
- Department of Infectious Disease, Imperial College London, London, UK
| | - Sandra M Newton
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Michael Levin
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Imperial College London, London, UK.
- Centre for Paediatrics and Child Health, Imperial College London, London, UK.
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48
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Hong GH, Guan Q, Peng H, Luo XH, Mao Q. Identification and validation of a T-cell-related MIR600HG/hsa-mir-21-5p competing endogenous RNA network in tuberculosis activation based on integrated bioinformatics approaches. Front Genet 2022; 13:979213. [PMID: 36204312 PMCID: PMC9531151 DOI: 10.3389/fgene.2022.979213] [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: 06/27/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: T cells play critical roles in the progression of tuberculosis (TB); however, knowledge regarding these molecular mechanisms remains inadequate. This study constructed a critical ceRNA network was constructed to identify the potentially important role of TB activation via T-cell regulation. Methods: We performed integrated bioinformatics analysis in a randomly selected training set from the GSE37250 dataset. After estimating the abundance of 18 types of T cells using ImmuCellAI, critical T-cell subsets were determined by their diagnostic accuracy in distinguishing active from latent TB. We then identified the critical genes associated with T-cell subsets in TB activation through co-expression analysis and PPI network prediction. Then, the ceRNA network was constructed based on RNA complementarity detection on the DIANA-LncBase and mirDIP platform. The gene biomarkers included in the ceRNA network were lncRNA, miRNA, and targeting mRNA. We then applied an elastic net regression model to develop a diagnostic classifier to assess the significance of the gene biomarkers in clinical applications. Internal and external validations were performed to assess the repeatability and generalizability. Results: We identified CD4+ T, Tr1, nTreg, iTreg, and Tfh as T cells critical for TB activation. A ceRNA network mediated by the MIR600HG/hsa-mir-21-5p axis was constructed, in which the significant gene cluster regulated the critical T subsets in TB activation. MIR600HG, hsa-mir-21-5p, and five targeting mRNAs (BCL11B, ETS1, EPHA4, KLF12, and KMT2A) were identified as gene biomarkers. The elastic net diagnostic classifier accurately distinguished active TB from latent. The validation analysis confirmed that our findings had high generalizability in different host background cases. Conclusion: The findings of this study provided novel insight into the underlying mechanisms of TB activation and identifying prospective biomarkers for clinical applications.
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Affiliation(s)
- Guo-Hu Hong
- Department of Infectious Disease, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Qing Guan
- Department of Dermatology, The First People’s Hospital of Guiyang, Guiyang, China
| | - Hong Peng
- Department of Infectious Disease, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Xin-Hua Luo
- Department of Infectious Disease, Guizhou Provincial People’s Hospital, Guiyang, China
- *Correspondence: Xin-Hua Luo, ; Qing Mao,
| | - Qing Mao
- Department of Infectious Disease, The First Hospital Affiliated to Army Medical University, Chongqing, China
- *Correspondence: Xin-Hua Luo, ; Qing Mao,
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49
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Are mRNA based transcriptomic signatures ready for diagnosing tuberculosis in the clinic? - A review of evidence and the technological landscape. EBioMedicine 2022; 82:104174. [PMID: 35850011 PMCID: PMC9294474 DOI: 10.1016/j.ebiom.2022.104174] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/11/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Funding
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50
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Kaforou M, Broderick C, Vito O, Levin M, Scriba TJ, Seddon JA. Transcriptomics for child and adolescent tuberculosis. Immunol Rev 2022; 309:97-122. [PMID: 35818983 PMCID: PMC9540430 DOI: 10.1111/imr.13116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) in humans is caused by Mycobacterium tuberculosis (Mtb). It is estimated that 70 million children (<15 years) are currently infected with Mtb, with 1.2 million each year progressing to disease. Of these, a quarter die. The risk of progression from Mtb infection to disease and from disease to death is dependent on multiple pathogen and host factors. Age is a central component in all these transitions. The natural history of TB in children and adolescents is different to adults, leading to unique challenges in the development of diagnostics, therapeutics, and vaccines. The quantification of RNA transcripts in specific cells or in the peripheral blood, using high-throughput methods, such as microarray analysis or RNA-Sequencing, can shed light into the host immune response to Mtb during infection and disease, as well as understanding treatment response, disease severity, and vaccination, in a global hypothesis-free manner. Additionally, gene expression profiling can be used for biomarker discovery, to diagnose disease, predict future disease progression and to monitor response to treatment. Here, we review the role of transcriptomics in children and adolescents, focused mainly on work done in blood, to understand disease biology, and to discriminate disease states to assist clinical decision-making. In recent years, studies with a specific pediatric and adolescent focus have identified blood gene expression markers with diagnostic or prognostic potential that meet or exceed the current sensitivity and specificity targets for diagnostic tools. Diagnostic and prognostic gene expression signatures identified through high-throughput methods are currently being translated into diagnostic tests.
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Affiliation(s)
- Myrsini Kaforou
- Department of Infectious DiseaseImperial College LondonLondonUK
| | | | - Ortensia Vito
- Department of Infectious DiseaseImperial College LondonLondonUK
| | - Michael Levin
- Department of Infectious DiseaseImperial College LondonLondonUK
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of PathologyUniversity of Cape TownCape TownSouth Africa
| | - James A. Seddon
- Department of Infectious DiseaseImperial College LondonLondonUK
- Desmond Tutu TB Centre, Department of Paediatrics and Child HealthStellenbosch UniversityCape TownSouth Africa
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