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Qi X, Yang Q, Cai J, Wu J, Gao Y, Ruan Q, Shao L, Liu J, Zhou X, Zhang W, Jiang N, Wang S. Transcriptional profiling of human peripheral blood mononuclear cells in household contacts of pulmonary tuberculosis patients provides insights into mechanisms of Mycobacterium tuberculosis control and elimination. Emerg Microbes Infect 2024; 13:2295387. [PMID: 38088554 PMCID: PMC10763880 DOI: 10.1080/22221751.2023.2295387] [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: 07/16/2023] [Accepted: 12/12/2023] [Indexed: 12/31/2023]
Abstract
Household contacts (HHCs) of patients with active tuberculosis (ATB) are at higher risk of Mycobacterium tuberculosis (M. tuberculosis) infection. However, the immune factors responsible for different defense responses in HHCs are unknown. Hence, we aimed to evaluate transcriptome signatures in human peripheral blood mononuclear cells (PBMCs) of HHCs to aid risk stratification. We recruited 112 HHCs of ATB patients and followed them for 6 years. Among the HHCs, only 2 developed ATB, while the remaining HHCs were classified into three groups: (1) HHC-1 group (n = 23): HHCs with consistently positive T-SPOT.TB test, negative chest radiograph, and no clinical symptoms or evidence of ATB during the 6-year follow-up period; (2) HHC-2 group (n = 15): HHCs with an initial positive T-SPOT result that later became negative without evidence of ATB; (3) HHC-3 group (n = 14): HHCs with a consistently negative T-SPOT.TB test and no clinical or radiological evidence of ATB. HHC-2 and HHC-3 were combined as HHC-23 group for analysis. RNA sequencing (RNA-seq) in PBMCs, with and without purified protein derivative (PPD) stimulation, identified significant differences in gene signatures between HHC-1 and HHC-23. Gene ontology analysis revealed functions related to bacterial pathogens, leukocyte chemotaxis, and inflammatory and cytokine responses. Modules associated with clinical features in the HHC-23 group were linked to the IL-17 signaling pathway, ferroptosis, complement and coagulation cascades, and the TNF signaling pathway. Validation using real-time PCR confirmed key genes like ATG-7, CXCL-3, and TNFRSF1B associated with infection outcomes in HHCs. Our research enhances understanding of disease mechanisms in HHCs. HHCs with persistent latent tuberculosis infection (HHC-1) showed significantly different gene expression compared to HHCs with no M. tuberculosis infection (HHC-23). These findings can help identify HHCs at risk of developing ATB and guide targeted public health interventions.
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Affiliation(s)
- Xiao Qi
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Qingluan Yang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Jianpeng Cai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
- Department of Infectious Diseases, Jing'an District Central Hospital, Shanghai, People’s Republic of China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Yan Gao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Qiaoling Ruan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Lingyun Shao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Jun Liu
- Department of Laboratory medicine, Department of Infectious Diseases, Wuxi Fifth People’s Hospital Affiliated to Nanjing Medical University, Wuxi, People’s Republic of China
| | - Xueshi Zhou
- Department of Laboratory medicine, Department of Infectious Diseases, Wuxi Fifth People’s Hospital Affiliated to Nanjing Medical University, Wuxi, People’s Republic of China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
- Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai, People’s Republic of China
| | - Ning Jiang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Sen Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
- Department of Laboratory medicine, Department of Infectious Diseases, Wuxi Fifth People’s Hospital Affiliated to Nanjing Medical University, Wuxi, People’s Republic of China
- Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai, People’s Republic of China
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Vito O, Psarras S, Syggelou A, Wright VJ, Amanatidou V, Newton SM, Shailes H, Trochoutsou K, Tsagaraki M, Levin M, Kaforou M, Tsolia M. Novel RNA biomarkers improve discrimination of children with tuberculosis disease from those with non-TB pneumonia after in vitro stimulation. Front Immunol 2024; 15:1401647. [PMID: 39391304 PMCID: PMC11464340 DOI: 10.3389/fimmu.2024.1401647] [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: 03/15/2024] [Accepted: 09/04/2024] [Indexed: 10/12/2024] Open
Abstract
The diagnosis of pediatric tuberculosis (TB) poses a challenge for clinical teams worldwide. TB-mediated changes in the expression of host genes in the peripheral blood can serve as diagnostic biomarkers and can provide better insights into the host immune mechanisms of childhood TB. Peripheral blood mononuclear cells (PBMCs) from children (n=102) with microbiologically confirmed TB disease, TB infection (TBI), pneumonia, and healthy controls (HC) were stimulated with either the Purified Protein Derivative (PPD) or the Early Secretory Antigen 6kDa-Culture Filtrate Protein 10 (ESAT6-CFP10) complex of Mycobacterium tuberculosis (Mtb). RNA was extracted and quantified using gene expression microarrays. Differential expression analysis was performed comparing microbiologically confirmed TB to the other diagnostic groups for the stimulated and unstimulated samples. Using variable selection, we identified sparse diagnostic gene signatures; one gene (PID1) was able to distinguish TB from pneumonia after ESAT6-CFP10 stimulation with an AUC of 100% in the test set, while a combination of two genes (STAT1 and IFI44) achieved an AUC of 91.7% (CI95% 75.0%-100%) in the test set after PPD stimulation. The number of significantly differentially expressed (SDE) genes was higher when contrasting TB to pneumonia or HC in stimulated samples, compared to unstimulated ones, leading to a larger pool of candidate diagnostic biomarkers. Our approach provides enlightened aspects of peripheral TB-specific responses and can form the basis for a point of care test meeting the World Health Organization (WHO) Target Product Profile (TPP) for pediatric TB.
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Affiliation(s)
- Ortensia Vito
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Centre for Pediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Stelios Psarras
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens , Athens, Greece
| | - Angeliki Syggelou
- Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children’s Hospital, Athens, Greece
| | - Victoria J. Wright
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Centre for Pediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Virginia Amanatidou
- Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children’s Hospital, Athens, Greece
| | - Sandra M. Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Centre for Pediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Hannah Shailes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Centre for Pediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Katerina Trochoutsou
- Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children’s Hospital, Athens, Greece
| | - Maria Tsagaraki
- Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children’s Hospital, Athens, Greece
| | - Michael Levin
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Centre for Pediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Myrsini Kaforou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Centre for Pediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Maria Tsolia
- Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children’s Hospital, Athens, Greece
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Mousavian Z, Folkesson E, Fröberg G, Foroogh F, Correia-Neves M, Bruchfeld J, Källenius G, Sundling C. A protein signature associated with active tuberculosis identified by plasma profiling and network-based analysis. iScience 2022; 25:105652. [PMID: 36561889 PMCID: PMC9763869 DOI: 10.1016/j.isci.2022.105652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/19/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Annually, approximately 10 million people are diagnosed with active tuberculosis (TB), and 1.4 million die of the disease. If left untreated, each person with active TB will infect 10-15 new individuals. The lack of non-sputum-based diagnostic tests leads to delayed diagnoses of active pulmonary TB cases, contributing to continued disease transmission. In this exploratory study, we aimed to identify biomarkers associated with active TB. We assessed the plasma levels of 92 proteins associated with inflammation in individuals with active TB (n = 20), latent TB (n = 14), or healthy controls (n = 10). Using co-expression network analysis, we identified one module of proteins with strong association with active TB. We removed proteins from the module that had low abundance or were associated with non-TB diseases in published transcriptomic datasets, resulting in a 12-protein plasma signature that was highly enriched in individuals with pulmonary and extrapulmonary TB and was further associated with disease severity.
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Affiliation(s)
- Zaynab Mousavian
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran
| | - Elin Folkesson
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Gabrielle Fröberg
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Fariba Foroogh
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Margarida Correia-Neves
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga, Portugal
| | - Judith Bruchfeld
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Gunilla Källenius
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christopher Sundling
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Corresponding author
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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: 20] [Impact Index Per Article: 6.7] [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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5
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Marete A, Ariel O, Ibeagha-Awemu E, Bissonnette N. Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression. Front Vet Sci 2021; 8:639053. [PMID: 33969037 PMCID: PMC8100051 DOI: 10.3389/fvets.2021.639053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/15/2021] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease. Weight loss, diarrhea, and a gradual drop in milk production characterize the disease's clinical phase, culminating in death. Several studies have characterized long non-coding RNA (lncRNA) in bovine tissues, and a previous study characterizes (lncRNA) in macrophages infected with MAP in vitro. In this study, we aim to characterize the lncRNA in macrophages from cows naturally infected with MAP. From 15 herds, feces and blood samples were collected for each cow older than 24 months, twice yearly over 3–5 years. Paired samples were analyzed by fecal PCR and blood ELISA. We used RNA-seq data to study lncRNA in macrophages from 33 JD(+) and 33 JD(–) dairy cows. We performed RNA-seq analysis using the “new Tuxedo” suite. We characterized lncRNA using logistic regression and multilayered neural networks and used DESeq2 for differential expression analysis and Panther and Reactome classification systems for gene ontology (GO) analysis. The study identified 13,301 lncRNA, 605 of which were novel lncRNA. We found seven genes close to differentially expressed lncRNA, including CCDC174, ERI1, FZD1, TWSG1, ZBTB38, ZNF814, and ZSCAN4. None of the genes associated with susceptibility to JD have been cited in the literature. LncRNA target genes were significantly enriched for biological process GO terms involved in immunity and nucleic acid regulation. These include the MyD88 pathway (TLR5), GO:0043312 (neutrophil degranulation), GO:0002446 (neutrophil-mediated immunity), and GO:0042119 (neutrophil activation). These results identified lncRNA with potential roles in host immunity and potential candidate genes and pathways through which lncRNA might function in response to MAP infection.
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Affiliation(s)
- Andrew Marete
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Olivier Ariel
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.,Faculty of Science, Sherbrooke University, Sherbrooke, QC, Canada
| | - Eveline Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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Sivakumaran D, Ritz C, Gjøen JE, Vaz M, Selvam S, Ottenhoff THM, Doherty TM, Jenum S, Grewal HMS. Host Blood RNA Transcript and Protein Signatures for Sputum-Independent Diagnostics of Tuberculosis in Adults. Front Immunol 2021; 11:626049. [PMID: 33613569 PMCID: PMC7891042 DOI: 10.3389/fimmu.2020.626049] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022] Open
Abstract
To achieve the ambitious targets for tuberculosis (TB) prevention, care, and control stated by the End TB Strategy, new health care strategies, diagnostic tools are warranted. Host-derived biosignatures are explored for their TB diagnostic potential in accordance with the WHO target product profiles (TPPs) for point-of-care (POC) testing. We aimed to identify sputum-independent TB diagnostic signatures in newly diagnosed adult pulmonary-TB (PTB) patients recruited in the context of a prospective household contact cohort study conducted in Andhra Pradesh, India. Whole-blood mRNA samples from 158 subjects (PTB, n = 109; age-matched household controls, n = 49) were examined by dual-color Reverse-Transcriptase Multiplex Ligation-dependent Probe-Amplification (dcRT-MLPA) for the expression of 198 pre-defined genes and a Mesoscale discovery assay for the concentration of 18 cytokines/chemokines in TB-antigen stimulated QuantiFERON supernatants. To identify signatures, we applied a two-step approach; in the first step, univariate filtering was used to identify and shortlist potentially predictive biomarkers; this step may be seen as removing redundant biomarkers. In the second step, a logistic regression approach was used such that group membership (PTB vs. household controls) became the binary response in a Lasso regression model. We identified an 11-gene signature that distinguished PTB from household controls with AUCs of ≥0.98 (95% CIs: 0.94–1.00), and a 4-protein signature (IFNγ, GMCSF, IL7 and IL15) that differentiated PTB from household controls with AUCs of ≥0.87 (95% CIs: 0.75–1.00), in our discovery cohort. Subsequently, we evaluated the performance of the 11-gene signature in two external validation data sets viz, an independent cohort at the Glenfield Hospital, University Hospitals of Leicester NHS Trust, Leicester, UK (GSE107994 data set), and the Catalysis treatment response cohort (GSE89403 data set) from South Africa. The 11-gene signature validated and distinguished PTB from healthy and asymptomatic M. tuberculosis infected household controls in the GSE107994 data set, with an AUC of 0.95 (95% CI: 0.91–0.98) and 0.94 (95% CI: 0.89–0.98). More interestingly in the GSE89403 data set, the 11-gene signature distinguished PTB from household controls and patients with other lung diseases with an AUC of 0.93 (95% CI: 0.87–0.99) and 0.73 (95% CI: 0.56–0.89). These criteria meet the WHO TTP benchmarks for a non–sputum-based triage test for TB diagnosis. We suggest that further validation is required before clinical implementation of the 11-gene signature we have identified markers will be possible.
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Affiliation(s)
- Dhanasekaran Sivakumaran
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, University of Bergen, Bergen, Norway
| | - Christian Ritz
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - John Espen Gjøen
- Department of Paediatrics, Haukeland University Hospital, Bergen, Norway
| | - Mario Vaz
- Department of Physiology, St. John's Medical College and Division of Health and Humanities, St. John's Research Institute, Bangalore, India
| | - Sumithra Selvam
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, India
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | | | - Synne Jenum
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Harleen M S Grewal
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, University of Bergen, Bergen, Norway
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Ai JW, Zhang H, Zhou Z, Weng S, Huang H, Wang S, Shao L, Gao Y, Wu J, Ruan Q, Wang F, Jiang N, Chen J, Zhang W. Gene expression pattern analysis using dual-color RT-MLPA and integrative genome-wide association studies of eQTL for tuberculosis suscepitibility. Respir Res 2021; 22:23. [PMID: 33472618 PMCID: PMC7816316 DOI: 10.1186/s12931-020-01612-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/29/2020] [Indexed: 01/06/2023] Open
Abstract
Background When infected with Mycobacterium tuberculosis, only a small proportion of the population will develop active TB, and the role of host genetic factors in different TB infection status was not fully understood. Methods Forty-three patients with active tuberculosis and 49 with latent tuberculosis were enrolled in the prospective cohort. Expressing levels of 27 candidate mRNAs, which were previously demonstrated to differentially expressed in latent and active TB, were measured by dual color reverse transcription multiplex ligation dependent probe amplification assay (dcRT-MLPA). Using expression levels of these mRNAs as quantitative traits, associations between expression abundance and genome-wild single nucleotide polymorphisms (SNPs) were calculated. Finally, identified candidate SNPs were further assessed for their associations with TB infection status in a validation cohort with 313 Chinese Han cases. Results We identified 9 differentially expressed mRNAs including il7r, il4, il8, tnfrsf1b, pgm5, ccl19, il2ra, marco and fpr1 in the prospective cohort. Through expression quantitative trait loci mapping, we screened out 8 SNPs associated with these mRNAs. Then, CG genotype of the SNP rs62292160 was finally verified to be significantly associated with higher transcription levels of IL4 in LTBI than in TB patients. Conclusion We reported that the SNP rs62292160 in Chinese Han population may link to higher expression of il4 in latent tuberculosis. Our findings provided a new genetic variation locus for further exploration of the mechanisms of TB and a possible target for TB genetic susceptibility studies, which might aid the clinical decision to precision treatment of TB.
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Affiliation(s)
- Jing-Wen Ai
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Hanyue Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Zumo Zhou
- Department of Infectious Diseases, People's Hospital of Zhuji, 122 Huanshan South Road, Zhuji, 311800, China
| | - Shanshan Weng
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Heqing Huang
- Department of Infectious Diseases, People's Hospital of Zhuji, 122 Huanshan South Road, Zhuji, 311800, China
| | - Sen Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Lingyun Shao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Yan Gao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Jing Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Qiaoling Ruan
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Feifei Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering and Institute of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China.
| | - Jiazhen Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China.
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China.
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8
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Pediatric Tuberculosis: The Impact of "Omics" on Diagnostics Development. Int J Mol Sci 2020; 21:ijms21196979. [PMID: 32977381 PMCID: PMC7582311 DOI: 10.3390/ijms21196979] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is a major public health concern for all ages. However, the disease presents a larger challenge in pediatric populations, partially owing to the lack of reliable diagnostic standards for the early identification of infection. Currently, there are no biomarkers that have been clinically validated for use in pediatric TB diagnosis. Identification and validation of biomarkers could provide critical information on prognosis of disease, and response to treatment. In this review, we discuss how the “omics” approach has influenced biomarker discovery and the advancement of a next generation rapid point-of-care diagnostic for TB, with special emphasis on pediatric disease. Limitations of current published studies and the barriers to their implementation into the field will be thoroughly reviewed within this article in hopes of highlighting future avenues and needs for combating the problem of pediatric tuberculosis.
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9
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Combining host-derived biomarkers with patient characteristics improves signature performance in predicting tuberculosis treatment outcomes. Commun Biol 2020; 3:359. [PMID: 32647325 PMCID: PMC7347567 DOI: 10.1038/s42003-020-1087-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/18/2020] [Indexed: 11/08/2022] Open
Abstract
Tuberculosis (TB) is a global health concern. Treatment is prolonged, and patients on anti-TB therapy (ATT) often experience treatment failure for various reasons. There is an urgent need to identify signatures for early detection of failure and initiation of a treatment switch. We investigated how gene biomarkers and/or basic patient characteristics could be used to define signatures for treatment outcomes in Indian adult pulmonary-TB patients treated with standard ATT. Using blood samples at baseline, a 12-gene signature combined with information on gender, previously-diagnosed TB, severe thinness, smoking and alcohol consumption was highly predictive of treatment failure at 6 months. Likewise a 4-protein biomarker signature combined with the same patient characteristics was almost as highly predictive of treatment failure. Combining biomarkers and basic patient characteristics may be useful for predicting and hence identification of treatment failure at an early stage of TB therapy. Sivakumaran et al. show that a 12-gene signature combined with gender, previously diagnosed tuberculosis (TB), severe thinness, smoking, and alcohol consumption predict the treatment outcome at 6 months. This study suggests that the combination of biomarkers and basic patient characteristics may better predict the treatment failure at an early stage of TB therapy.
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10
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Ho J, Bokil NJ, Nguyen PTB, Nguyen TA, Liu MY, Hare N, Fox GJ, Saunders BM, Marks GB, Britton WJ. A transcriptional blood signature distinguishes early tuberculosis disease from latent tuberculosis infection and uninfected individuals in a Vietnamese cohort. J Infect 2020; 81:72-80. [PMID: 32330522 DOI: 10.1016/j.jinf.2020.03.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Global tuberculosis (TB) control is restricted by the failure to detect an estimated 3.3 million TB cases annually. In the majority of TB endemic settings, sputum smear microscopy is used to diagnose TB, but this test is insensitive for TB in its early stages. The objective of this study is to establish a concise gene signature that discriminates between individuals with early TB disease, latent TB infection (LTBI) and those without infection. METHODS This is a case control study nested within a cluster-randomised trial of population screening for active TB using Xpert MTB/RIF. Whole blood samples from 303 participants with active TB (97), LTBI (92) and uninfected individuals (114) were subject to transcriptomic analysis of selected target genes based on a systematic review of previous studies. RESULTS Analysis of 82 genes identified a pattern of differentially expressed genes in TB disease. A seven gene signature was identified that distinguished between TB disease and no TB disease with an AUC of 0.86 (95% CI: 0.80-0.91), and between TB disease from LTBI with an AUC of 0.88 (95% CI: 0.82-0.93). CONCLUSION This gene signature accurately distinguishes early TB disease from those without TB disease or infection, in the context of community-wide TB screening. It could be used as a non-sputum based screening tool or triage test to detect prevalent cases of TB in the community.
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Affiliation(s)
- Jennifer Ho
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, Australia; Centenary Institute, The University of Sydney, Sydney, Australia.
| | - Nilesh J Bokil
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Phuong Thi Bich Nguyen
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia
| | - Thu Anh Nguyen
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia
| | - Michael Y Liu
- The ithree Institute, University of Technology Sydney, Sydney, Australia
| | - Nathan Hare
- Centenary Institute, The University of Sydney, Sydney, Australia
| | - Greg J Fox
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Bernadette M Saunders
- Centenary Institute, The University of Sydney, Sydney, Australia; School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Guy B Marks
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, Australia
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, Australia; Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
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11
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Araujo Z, Palacios A, Enciso-Moreno L, Lopez-Ramos JE, Wide A, Waard JHD, Rivas-Santiago B, Serrano CJ, Bastian-Hernandez Y, Castañeda-Delgado JE, Enciso-Moreno JA. Evaluation of the transcriptional immune biomarkers in peripheral blood from Warao indigenous associate with the infection by Mycobacterium tuberculosis. Rev Soc Bras Med Trop 2019; 52:e20180516. [PMID: 31141056 DOI: 10.1590/0037-8682-0516-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/22/2019] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Biomarkers are critical tools for finding new approaches for controlling the spread of tuberculosis (TB), including for predicting the development of TB therapeutics, vaccines, and diagnostic tools. METHODS Expression of immune biomarkers was analyzed in peripheral blood cells stimulated and non-stimulated with M. tuberculosis antigens ESAT-6, CFP10 and TB7.7. in Warao indigenous individuals. These biomarkers may be able to differentiate TB states, such as active tuberculosis (ATB) cases and latent tuberculosis infection (LTBI) from non-infected controls (NIC). A real-time reverse transcription polymerase chain reaction (RT-qPCR) assay was performed on 100 blood samples under non-stimulation or direct ex vivo conditions (NS=50) and stimulation conditions (S=50). RESULTS The findings are shown as the median and interquartile range (IQR) of relative gene expression levels of IFN-γ, CD14, MMP9, CCR5, CCL11, CXCL9/MIG, and uPAR/PLAUR immune biomarkers. MMP9 levels were significantly higher in the LTBI-NS and LTBI-S groups compared with the NIC-NS and NIC-S groups. However, CCR5 levels were significantly lower in the LTBI-S group compared with both NIC-NS and NIC-S groups. CCL11 levels were significantly lower in the LTBI-S group compared with the NIC-NS group. CONCLUSIONS Preliminary findings showed that MMP9 immune biomarkers separated LTBI indigenous individuals from NIC indigenous individuals, while CCR5, CCL11, CD14, and IFN-γ did not differentiate TB states from NIC. MMP9 may be useful as a potential biomarker for LTBI and new infected case detection among Warao indigenous individuals at high risk of developing the disease. It may also be used to halt the epidemic, which will require further validation in larger studies.
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Affiliation(s)
- Zaida Araujo
- Laboratorio de Inmunología de Enfermedades Infecciosas, Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Caracas, Venezuela
| | - Andrea Palacios
- Laboratorio de Inmunología de Enfermedades Infecciosas, Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Caracas, Venezuela
| | - Leonor Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Mexico
| | - Juan Ernesto Lopez-Ramos
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Mexico.,Universidad Autónoma de Aguascalientes, Aguascalientes, Mexico
| | - Albina Wide
- Laboratorio de Biotecnología, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Jacobus Henri de Waard
- Laboratorio de Tuberculosis, Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Caracas, Venezuela
| | - Bruno Rivas-Santiago
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Mexico
| | - Carmen Judith Serrano
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Mexico
| | - Yadira Bastian-Hernandez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Mexico.,Cátedras CONACYT, Consejo Nacional de Ciencia y Tecnología, México
| | - Julio Enrique Castañeda-Delgado
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Mexico.,Cátedras CONACYT, Consejo Nacional de Ciencia y Tecnología, México
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12
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Land KJ. The Many Roads to an Ideal Paper-based Device. PAPER-BASED DIAGNOSTICS 2018. [PMCID: PMC7119996 DOI: 10.1007/978-3-319-96870-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The recent Zika and Ebola virus outbreaks highlight the need for low-cost diagnostics that can be rapidly deployed and used outside of established clinical infrastructure. This demand for robust point-of-care (POC) diagnostics is further driven by the increasing burden of drug-resistant diseases, concern for food and water safety, and bioterrorism. As has been discussed in previous chapters, paper-based tests provide a simple and compelling solution to such needs.
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Affiliation(s)
- Kevin J. Land
- Council for Scientific and Industrial Research, Pretoria, South Africa
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13
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Togun TO, MacLean E, Kampmann B, Pai M. Biomarkers for diagnosis of childhood tuberculosis: A systematic review. PLoS One 2018; 13:e0204029. [PMID: 30212540 PMCID: PMC6136789 DOI: 10.1371/journal.pone.0204029] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
Introduction As studies of biomarkers of tuberculosis (TB) disease provide hope for a simple, point-of-care test, we aimed to synthesize evidence on biomarkers for diagnosis of TB in children and compare their accuracy to published target product profiles (TPP). Methods We conducted a systematic review of biomarkers for diagnosis of pulmonary TB in exclusively paediatric populations, defined as age less than 15 years. PubMed, EMBASE and Web of Science were searched for relevant publications from January 1, 2000 to November 27, 2017. Studies using mixed adult and paediatric populations or reporting biomarkers for extrapulmonary TB were excluded. Study quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies—2 (QUADAS-2) framework. No meta-analysis was done because the published childhood TB biomarkers studies were mostly early stage studies and highly heterogeneous. Results The 29 studies included in this systematic review comprise 20 case-control studies, six cohort studies and three cross-sectional studies. These studies reported diverse and heterogeneous forms of biomarkers requiring different types of clinical specimen and laboratory assays. Majority of the studies (27/29 [93%]) either did not meet the criteria in at least one of the four domains of the QUADAS-2 reporting framework or the assessment was unclear. However, the diagnostic performance of biomarkers reported in 22 studies met one or both of the WHO-recommended minimal targets of 66% sensitivity and 98% specificity for a new diagnostic test for TB disease in children, and/or 90% sensitivity and 70% specificity for a triage test. Conclusion We found that majority of the biomarkers for diagnosis of TB in children are promising but will need further refining and optimization to improve their performances. As new data are emerging, stronger emphasis should be placed on improving the design, quality and general reporting of future studies investigating TB biomarkers in children.
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Affiliation(s)
- Toyin Omotayo Togun
- McGill International TB Centre, and Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- * E-mail:
| | - Emily MacLean
- McGill International TB Centre, and Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Madhukar Pai
- McGill International TB Centre, and Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Manipal McGill Centre for Infectious Diseases, Manipal University, Manipal, India
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14
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Álvarez Álvarez C, Cabero Pérez MJ, Guerra Díez L, San Segundo Arribas D. [Results of the implementation of a protocol for outpatient management of the paediatric patient with tuberculosis]. J Healthc Qual Res 2018; 33:206-212. [PMID: 31610976 DOI: 10.1016/j.jhqr.2018.03.007] [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: 08/17/2017] [Revised: 03/03/2018] [Accepted: 03/26/2018] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To assess the results of the implementation of a protocol for the outpatient management of paediatric patients with tuberculosis, and to compare it with the previous approach. MATERIAL AND METHODS All patients younger than 14 years of age diagnosed with tuberculosis in Cantabria between 2005 and 2014 were included in the study. The pre-implementation period included patients admitted for gastric aspirate collection and to start treatment until 2010 (Pre-group). The post-implementation period was from 2010 onwards, using a protocol established for the outpatient management of these patients, with admission only being for clinical or social reasons, post-implantation period (Post-group). RESULTS A total of 82 patients were studied: 29 from the Pre-group and 53 from Post-group. The median age was 61 months (IQR 32.5-97.75). All patients in the Pre-group were systematically admitted, compared to 26.4% of the Post-group (P<.001). The mean hospital stay was higher (7.27±7.1 days) in the Pre-group than in Post-group (3.4±11.46 days) (P<.0001). Only in 6.9% of patients from Pre-group were the 3 microbiological samples recommended for diagnosis following the international guidelines were provided, whereas they were provided by 73.58% patients from Post-group (P<.001). Of the cultures performed, 26.6% were positive for Mycobacterium tuberculosis, 37.5% of the Pre-group and 21.6% of the Post-group (P=.121). No significant differences were observed between the groups in other parameters related to treatment such as, therapeutic adherence, treatment not adjusted to the guidelines, treatment withdrawal or relapse.. DISCUSSION Although guidelines recommend three microbiological samples for culture, no superior microbiological isolation was detected despite the increased number of samples collected. The management in hospital clinics of patients with suspected tuberculosis with stable clinical situation show similar or better clinical and microbiological results to the previous management, with lower hospital admission rate and with the subsequent cost savings.
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Affiliation(s)
- C Álvarez Álvarez
- Unidad de Infectología Pediátrica, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España.
| | - M J Cabero Pérez
- Unidad de Neumología Pediátrica, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España
| | - L Guerra Díez
- Unidad de Urgencias Pediátricas, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España
| | - D San Segundo Arribas
- Servicio de Inmunología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Cantabria, España
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15
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Abstract
Autophagy is an evolutionarily conserved degradation pathway for cells to maintain homeostasis, produce energy, degrade misfolded proteins and damaged organelles, and fight against intracellular pathogens. The process of autophagy entails the isolation of cytoplasmic cargo into double membrane bound autophagosomes that undergo maturation by fusion with endosomes and lysosomes to obtain degradation capacity. RAB proteins regulate intracellular vesicle trafficking events including autophagy. RAB24 is an atypical RAB protein that is required for the clearance of late autophagic vacuoles under basal conditions. RAB24 has also been connected to several diseases including ataxia, cancer and tuberculosis. This review gives a short summary on autophagy and RAB proteins, and an overview on the current knowledge on the roles of RAB24 in autophagy and disease.
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Affiliation(s)
- Päivi Ylä-Anttila
- a Department of Biosciences , University of Helsinki , Helsinki , Finland
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16
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Shores DR, Everett AD. Children as Biomarker Orphans: Progress in the Field of Pediatric Biomarkers. J Pediatr 2018; 193:14-20.e31. [PMID: 29031860 PMCID: PMC5794519 DOI: 10.1016/j.jpeds.2017.08.077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/04/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Darla R Shores
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD.
| | - Allen D Everett
- Division of Cardiology, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD
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17
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Abstract
PURPOSE OF REVIEW Although tuberculosis (TB) causes much morbidity and mortality in children, diagnosis and treatment remain challenging. Recently, children have gained increasing attention in research and clinical trials driving improved contact management, case identification and treatment of both drug-susceptible and drug-resistant TB. This review highlights some recent advances. RECENT FINDINGS The tuberculin skin test is the most widely used test to distinguish Mycobacterium tuberculosis (M. tuberculosis) infection from active TB, however, using M. tuberculosis-specific, antigenic stimulation of CD4 and CD8 cells appear more effective. The use of Xpert MTB/RIF to identify M. tuberculosis in clinical samples, together with novel sampling methods have in part, overcome the difficulty of sampling and increased case identification capacity. Advances in treating both drug-susceptible and drug-resistant childhood TB show promise in being more paediatric friendly and improving adherence. Dosing strategies for drug-sensitive TB have improved with dispersible fixed drug combinations now available. In the treatment and prevention of drug-resistant TB, however, research involving the use of newer and more effective drugs currently recommended for adults, are still ongoing in children. SUMMARY The World Health Organization aims to end the TB epidemic by 2035 whereas the United Nations' Sustainable Developmental Goals sets this ambitious target for 2030. Therefore, adequate funding and implementing effective national TB programs must be prioritized, particularly in high-burden, low-income settings.
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18
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Haks MC, Bottazzi B, Cecchinato V, De Gregorio C, Del Giudice G, Kaufmann SHE, Lanzavecchia A, Lewis DJM, Maertzdorf J, Mantovani A, Sallusto F, Sironi M, Uguccioni M, Ottenhoff THM. Molecular Signatures of Immunity and Immunogenicity in Infection and Vaccination. Front Immunol 2017; 8:1563. [PMID: 29204145 PMCID: PMC5699440 DOI: 10.3389/fimmu.2017.01563] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/31/2017] [Indexed: 01/28/2023] Open
Abstract
Vaccinology aims to understand what factors drive vaccine-induced immunity and protection. For many vaccines, however, the mechanisms underlying immunity and protection remain incompletely characterized at best, and except for neutralizing antibodies induced by viral vaccines, few correlates of protection exist. Recent omics and systems biology big data platforms have yielded valuable insights in these areas, particularly for viral vaccines, but in the case of more complex vaccines against bacterial infectious diseases, understanding is fragmented and limited. To fill this gap, the EC supported ADITEC project (http://www.aditecproject.eu/; http://stm.sciencemag.org/content/4/128/128cm4.full) featured a work package on “Molecular signatures of immunity and immunogenicity,” aimed to identify key molecular mechanisms of innate and adaptive immunity during effector and memory stages of immune responses following vaccination. Specifically, technologies were developed to assess the human immune response to vaccination and infection at the level of the transcriptomic and proteomic response, T-cell and B-cell memory formation, cellular trafficking, and key molecular pathways of innate immunity, with emphasis on underlying mechanisms of protective immunity. This work intersected with other efforts in the ADITEC project. This review summarizes the main achievements of the work package.
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Affiliation(s)
- Mariëlle C Haks
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | | | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Corinne De Gregorio
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | - Jeroen Maertzdorf
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Alberto Mantovani
- Humanitas Clinical and Research Center, Rozzano, Italy.,Humanitas University, Department of Biomedical Sciences, Pieve Emanuele-Milan, Italy
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Marina Sironi
- Humanitas Clinical and Research Center, Rozzano, Italy
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Humanitas University, Department of Biomedical Sciences, Pieve Emanuele-Milan, Italy
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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19
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Gjøen JE, Jenum S, Sivakumaran D, Mukherjee A, Macaden R, Kabra SK, Lodha R, Ottenhoff THM, Haks MC, Doherty TM, Ritz C, Grewal HMS. Novel transcriptional signatures for sputum-independent diagnostics of tuberculosis in children. Sci Rep 2017; 7:5839. [PMID: 28724962 PMCID: PMC5517635 DOI: 10.1038/s41598-017-05057-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/24/2017] [Indexed: 11/20/2022] Open
Abstract
Pediatric tuberculosis (TB) is challenging to diagnose, confirmed by growth of Mycobacterium tuberculosis at best in 40% of cases. The WHO has assigned high priority to the development of non-sputum diagnostic tools. We therefore sought to identify transcriptional signatures in whole blood of Indian children, capable of discriminating intra-thoracic TB disease from other symptomatic illnesses. We investigated the expression of 198 genes in a training set, comprising 47 TB cases (19 definite/28 probable) and 36 asymptomatic household controls, and identified a 7- and a 10-transcript signature, both including NOD2, GBP5, IFITM1/3, KIF1B and TNIP1. The discriminatory abilities of the signatures were evaluated in a test set comprising 24 TB cases (17 definite/7 probable) and 26 symptomatic non-TB cases. In separating TB-cases from symptomatic non-TB cases, both signatures provided an AUC of 0.94 (95%CI, 0.88–1.00), a sensitivity of 91.7% (95%CI, 71.5–98.5) regardless of culture status, and 100% sensitivity for definite TB. The 7-transcript signature provided a specificity of 80.8% (95%CI, 60.0–92.7), and the 10-transcript signature a specificity of 88.5% (95%CI, 68.7–96.9%). Although warranting exploration and validation in other populations, our findings are promising and potentially relevant for future non-sputum based POC diagnostic tools for pediatric TB.
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Affiliation(s)
- John Espen Gjøen
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Synne Jenum
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | | | - Aparna Mukherjee
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ragini Macaden
- Division of Infectious Diseases, St. John's Research Institute, Koramangala, Bangalore, India
| | - Sushil K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Tom H M Ottenhoff
- Department of Infectious Diseases Group, Immunology and Immunogenetics of Bacterial Infectious Disease, Leiden University Medical Center, Leiden, The Netherlands
| | - Marielle C Haks
- Department of Infectious Diseases Group, Immunology and Immunogenetics of Bacterial Infectious Disease, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Christian Ritz
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark.
| | - Harleen M S Grewal
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway. .,Department of Microbiology, Haukeland University Hospital, University of Bergen, Bergen, Norway.
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20
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Abstract
Autophagy is an evolutionarily conserved degradation pathway for cells to maintain homeostasis, produce energy, degrade misfolded proteins and damaged organelles, and fight against intracellular pathogens. The process of autophagy entails the isolation of cytoplasmic cargo into double membrane bound autophagosomes that undergo maturation by fusion with endosomes and lysosomes to obtain degradation capacity. RAB proteins regulate intracellular vesicle trafficking events including autophagy. RAB24 is an atypical RAB protein that is required for the clearance of late autophagic vacuoles under basal conditions. RAB24 has also been connected to several diseases including ataxia, cancer and tuberculosis. This review gives a short summary on autophagy and RAB proteins, and an overview on the current knowledge on the roles of RAB24 in autophagy and disease.
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Affiliation(s)
- Päivi Ylä-Anttila
- a Department of Biosciences , University of Helsinki , Helsinki , Finland
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21
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Jenum S, Bakken R, Dhanasekaran S, Mukherjee A, Lodha R, Singh S, Singh V, Haks MC, Ottenhoff THM, Kabra SK, Doherty TM, Ritz C, Grewal HMS. BLR1 and FCGR1A transcripts in peripheral blood associate with the extent of intrathoracic tuberculosis in children and predict treatment outcome. Sci Rep 2016; 6:38841. [PMID: 27941850 PMCID: PMC5150239 DOI: 10.1038/srep38841] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/08/2016] [Indexed: 02/07/2023] Open
Abstract
Biomarkers reflecting the extent of Mycobacterium tuberculosis-induced pathology and normalization during anti-tuberculosis treatment (ATT) would considerably facilitate trials of new treatment regimens and the identification of patients with treatment failure. Therefore, in a cohort of 99 Indian children with intrathoracic tuberculosis (TB), we performed blood transcriptome kinetic analysis during ATT to explore 1) the association between transcriptional biomarkers in whole blood (WB) and the extent of TB disease at diagnosis and treatment outcomes at 2 and 6 months, and 2) the potential of the biomarkers to predict treatment response at 2 and 6 months. We present the first data on the association between transcriptional biomarkers and the extent of TB disease as well as outcome of ATT in children: Expression of three genes down-regulated on ATT (FCGR1A, FPR1 and MMP9) exhibited a positive correlation with the extent of TB disease, whereas expression of eight up-regulated genes (BCL, BLR1, CASP8, CD3E, CD4, CD19, IL7R and TGFBR2) exhibited a negative correlation with the extent of disease. Baseline levels of these transcripts displayed an individual capacity >70% to predict the six-month treatment outcome. In particular, BLR1 and FCGR1A seem to have a potential in monitoring and perhaps tailoring future antituberculosis therapy.
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Affiliation(s)
- Synne Jenum
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Rasmus Bakken
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - S. Dhanasekaran
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Aparna Mukherjee
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sarman Singh
- Division of Clinical Microbiology & Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Varinder Singh
- Department of Pediatrics, Kalawati Saran Children Hospital, New Delhi, India
| | - Marielle C. Haks
- Department of Infectious Diseases Group, Immunology and Immunogenetics of Bacterial Infectious Disease, Leiden University Medical Center, The Netherland
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases Group, Immunology and Immunogenetics of Bacterial Infectious Disease, Leiden University Medical Center, The Netherland
| | - S. K. Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | | | - Christian Ritz
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Denmark
| | - Harleen M. S. Grewal
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland university hospital, University of Bergen, N-5021, Norway
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Amaya C, Militello RD, Calligaris SD, Colombo MI. Rab24 interacts with the Rab7/Rab interacting lysosomal protein complex to regulate endosomal degradation. Traffic 2016; 17:1181-1196. [PMID: 27550070 DOI: 10.1111/tra.12431] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 08/17/2016] [Accepted: 08/17/2016] [Indexed: 12/11/2022]
Abstract
Endocytosis is a multistep process engaged in extracellular molecules internalization. Several proteins including the Rab GTPases family coordinate the endocytic pathway. The small GTPase Rab7 is present in late endosome (LE) compartments being a marker of endosome maturation. The Rab interacting lysosomal protein (RILP) is a downstream effector of Rab7 that recruits the functional dynein/dynactin motor complex to late compartments. In the present study, we have found Rab24 as a component of the endosome-lysosome degradative pathway. Rab24 is an atypical protein of the Rab GTPase family, which has been attributed a function in vesicle trafficking and autophagosome maturation. Using a model of transiently expressed proteins in K562 cells, we found that Rab24 co-localizes in vesicular structures labeled with Rab7 and LAMP1. Moreover, using a dominant negative mutant of Rab24 or a siRNA-Rab24 we showed that the distribution of Rab7 in vesicles depends on a functional Rab24 to allow DQ-BSA protein degradation. Additionally, by immunoprecipitation and pull down assays, we have demonstrated that Rab24 interacts with Rab7 and RILP. Interestingly, overexpression of the Vps41 subunit from the homotypic fusion and protein-sorting (HOPS) complex hampered the co-localization of Rab24 with RILP or with the lysosomal GTPase Arl8b, suggesting that Vps41 would affect the Rab24/RILP association. In summary, our data strongly support the hypothesis that Rab24 forms a complex with Rab7 and RILP on the membranes of late compartments. Our work provides new insights into the molecular function of Rab24 in the last steps of the endosomal degradative pathway.
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Affiliation(s)
- Celina Amaya
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Rodrigo D Militello
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Sebastián D Calligaris
- Centro de Medicina Regenerativa, Facultad de Medicina, Universidad del Desarrollo Clínica Alemana, Santiago, Chile
| | - María I Colombo
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina.
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23
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Associations between systemic inflammation, mycobacterial loads in sputum and radiological improvement after treatment initiation in pulmonary TB patients from Brazil: a prospective cohort study. BMC Infect Dis 2016; 16:368. [PMID: 27494953 PMCID: PMC4974760 DOI: 10.1186/s12879-016-1736-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/27/2016] [Indexed: 12/26/2022] Open
Abstract
Background Mycobacterium tuberculosis infection is known to cause inflammation and lung tissue damage in high-risk populations. Nevertheless, direct associations between mycobacterial loads, systemic inflammation and pulmonary lesions upon treatment initiation have not been fully characterized. In the present exploratory study, we prospectively depict the immune profile, microbial clearance and evolution of radiographic lesions in a pulmonary tuberculosis (PTB) patient cohort before and 60 days after anti-tuberculous treatment (ATT) initiation. Methods Circulating levels of cytokines (IL-2, IL-4, IL-6, IL-10, IFN-γ, TNF-α) and C-reactive protein (CRP), as well as values of erythrocyte sedimentation rate (ESR) were measured in cryopreserved serum samples obtained from 73 PTB patients at pre-ATT and day 60 of treatment. Changes of the immune profile over time were compared with mycobacterial loads in sputum and culture conversion at day 60 of ATT. Additional analyses tested associations between improvement of chest radiographic lesions at day 60 and pre-treatment status of inflammation and mycobacterial loads. Results Within the inflammatory parameters evaluated, values of CRP, IL-2, IL-4, TNF-α and ESR significantly decreased upon treatment initiation. On the converse, IL-10 levels substantially increased at day 60 of ATT, whereas concentrations of IL-6 and IFN-γ remained unchanged. Multidimensional analyses revealed that ESR, IL-2, IL-4 and CRP were the parameters with the highest power to discriminate individuals before and after treatment initiation. We further demonstrated that higher bacterial loads in sputum at pre-ATT were associated with increased systemic inflammation and higher risk for positive M. tuberculosis sputum cultures at day 60 of treatment. Furthermore, we found that pre-ATT mycobacterial loads in sputum and systemic inflammation synergistically associated with the status of radiographic lesions during treatment (Relative risk for chest X-ray improvement: 10.0, 95 % confidence interval: 2.4–40.0, P = 0.002). Conclusions M. tuberculosis loads in sputum are directly associated to the status of systemic inflammation and potentially impact the immune profile, culture conversion and evolution of lung lesions upon ATT initiation. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1736-3) contains supplementary material, which is available to authorized users.
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Hofman S, Segers MM, Ghimire S, Bolhuis MS, Sturkenboom MGG, Van Soolingen D, Alffenaar JWC. Emerging drugs and alternative possibilities in the treatment of tuberculosis. Expert Opin Emerg Drugs 2016; 21:103-16. [PMID: 26848966 DOI: 10.1517/14728214.2016.1151000] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Tuberculosis (TB) remains a global health problem. Drug resistance, treatment duration, complexity, and adverse drug reactions associated with anti-TB regimens are associated with treatment failure, prolonged infectiousness and relapse. With the current set of anti-TB drugs the goal to end TB has not been met. New drugs and new treatment regimens are needed to eradicate TB. AREAS COVERED Literature was explored to select publications on drugs currently in phase II and phase III trials. These include new chemical entities, immunotherapy, established drugs in new treatment regimens and vaccines for the prophylaxis of TB. EXPERT OPINION Well designed trials, with detailed pharmacokinetic/pharmacodynamic analysis, in which information on drug exposure and drug susceptibility of the entire anti-TB regimen is included, in combination with long-term follow-up will provide relevant data to optimize TB treatment. The new multi arm multistage trial design could be used to test new combinations of compounds, immunotherapy and therapeutic vaccines. This new approach will both reduce the number of patients exposed to inferior treatment and the financial burden. Moreover, it will speed up drug evaluation. Considering the investments involved in development of new drugs it is worthwhile to thoroughly investigate existing, non-TB drugs in new regimens.
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Affiliation(s)
- S Hofman
- a University of Groningen , University Medical Center Groningen, Department of Clinical Pharmacy and Pharmacology , Groningen , the Netherlands
| | - M M Segers
- a University of Groningen , University Medical Center Groningen, Department of Clinical Pharmacy and Pharmacology , Groningen , the Netherlands
| | - S Ghimire
- a University of Groningen , University Medical Center Groningen, Department of Clinical Pharmacy and Pharmacology , Groningen , the Netherlands
| | - M S Bolhuis
- a University of Groningen , University Medical Center Groningen, Department of Clinical Pharmacy and Pharmacology , Groningen , the Netherlands
| | - M G G Sturkenboom
- a University of Groningen , University Medical Center Groningen, Department of Clinical Pharmacy and Pharmacology , Groningen , the Netherlands
| | - D Van Soolingen
- b Departments of Pulmonary Diseases and Medical Microbiology , Nijmegen Medical Center, Radboud University , Nijmegen , The Netherlands.,c National Tuberculosis Reference Laboratory , National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands
| | - J W C Alffenaar
- a University of Groningen , University Medical Center Groningen, Department of Clinical Pharmacy and Pharmacology , Groningen , the Netherlands
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