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Rotundo S, Tassone MT, Serapide F, Russo A, Trecarichi EM. Incipient tuberculosis: a comprehensive overview. Infection 2024; 52:1215-1222. [PMID: 38589748 PMCID: PMC11289152 DOI: 10.1007/s15010-024-02239-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024]
Abstract
In the context of the evolving global health landscape shaped by the COVID-19 pandemic, tuberculosis (TB) is gaining renewed attention as a reemerging threat even in low-endemic countries. Immunological tests such as the tuberculin skin test (TST) and interferon-gamma release assay (IGRA) are pivotal in identifying tuberculosis infection (TBI). However, their inability to distinguish between past and ongoing infection poses a diagnostic challenge, possibly leading to the unnecessary treatment of a significant portion of the population with potential side effects. This review delves into the concept of incipient tuberculosis (ITB), a dynamic, presymptomatic stage characterized by heightened Mycobacterium tuberculosis complex (MTC) metabolic activity and replication that result in minimal radiological changes, signifying a transitional state between TBI and TB. Key focus areas include epidemiological factors, underlying pathogenesis, imaging findings, and the ongoing challenges in the identification of individuals with ITB through the development of new biomarkers and the use of whole-genome sequencing-based analyses to implement early treatment strategies.
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Affiliation(s)
- Salvatore Rotundo
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy.
| | - Maria Teresa Tassone
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Francesca Serapide
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
- Infectious and Tropical Disease Unit, "Renato Dulbecco" Teaching Hospital, Catanzaro, Italy
| | - Alessandro Russo
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
- Infectious and Tropical Disease Unit, "Renato Dulbecco" Teaching Hospital, Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
- Infectious and Tropical Disease Unit, "Renato Dulbecco" Teaching Hospital, Catanzaro, Italy
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2
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Jia Q, Wu Y, Huang Y, Bai X. New genetic biomarkers from transcriptome RNA-sequencing for Mycobacterium tuberculosis complex and Mycobacterium avium complex infections by bioinformatics analysis. Sci Rep 2024; 14:17385. [PMID: 39075154 PMCID: PMC11286745 DOI: 10.1038/s41598-024-68242-9] [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: 05/20/2024] [Accepted: 07/22/2024] [Indexed: 07/31/2024] Open
Abstract
The study aims to accurately identify differentially expressed genes (DEGs) and biological pathways in mycobacterial infections through bioinformatics for deeper disease understanding. Differentially expressed genes (DEGs) was explored by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Unique DEGs were submitted on least absolute shrinkage and selection operator (LASSO) regression analysis. 1,057 DEGs from two GSE datasets were identified, which were closely connected with NTM/ latent TB infection (LTBI)/active TB disease (ATB). It was demonstrated that these DEGs are mainly associated with detoxification processes, and virus and bacterial infections. Moreover, the METTL7B gene was the most informative marker for distinguishing LTBI and ATB with an area under the curve (AUC) of 0.983 (95%CI: 0.964 to 1). The significantly upregulated HBA1/2 genes were the most informative marker for distinguishing between individuals of IGRA-HC/NTM and LTBI (P < 0.001). Moreover, the upregulated HBD gene was also differ between IGRA-HC/NTM and ATB (P < 0.001). We have identified gene signatures associated with Mycobacterium infection in whole blood, which could be significant for understanding the molecular mechanisms and diagnosis of NTM, LTBI, or ATB.
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Affiliation(s)
- Qingjun Jia
- Department of Tuberculosis Control and Prevention, Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Mingshi 568#, Shangcheng, Hangzhou, 310021, Zhejiang, China.
| | - Yifei Wu
- Department of Tuberculosis Control and Prevention, Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Mingshi 568#, Shangcheng, Hangzhou, 310021, Zhejiang, China
| | - Yinyan Huang
- Department of Tuberculosis Control and Prevention, Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Mingshi 568#, Shangcheng, Hangzhou, 310021, Zhejiang, China
| | - Xuexin Bai
- Department of Tuberculosis Control and Prevention, Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Mingshi 568#, Shangcheng, Hangzhou, 310021, Zhejiang, China
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3
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Meade RK, Smith CM. Immunological roads diverged: mapping tuberculosis outcomes in mice. Trends Microbiol 2024:S0966-842X(24)00170-7. [PMID: 39034171 DOI: 10.1016/j.tim.2024.06.007] [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: 05/06/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
The journey from phenotypic observation to causal genetic mechanism is a long and challenging road. For pathogens like Mycobacterium tuberculosis (Mtb), which causes tuberculosis (TB), host-pathogen coevolution has spanned millennia, costing millions of human lives. Mammalian models can systematically recapitulate host genetic variation, producing a spectrum of disease outcomes. Leveraging genome sequences and deep phenotyping data from infected mouse genetic reference populations (GRPs), quantitative trait locus (QTL) mapping approaches have successfully identified host genomic regions associated with TB phenotypes. Here, we review the ongoing optimization of QTL mapping study design alongside advances in mouse GRPs. These next-generation resources and approaches have enabled identification of novel host-pathogen interactions governing one of the most prevalent infectious diseases in the world today.
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Affiliation(s)
- Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA.
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4
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Lee AM, Nathan CF. Type I interferon exacerbates Mycobacterium tuberculosis induced human macrophage death. EMBO Rep 2024; 25:3064-3089. [PMID: 38866980 PMCID: PMC11239827 DOI: 10.1038/s44319-024-00171-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
Type I interferons (IFN-I) are implicated in exacerbation of tuberculosis (TB), but the mechanisms are unclear. Mouse macrophages infected with Mycobacterium tuberculosis (Mtb) produce IFN-I, which contributes to their death. Here we investigate whether the same is true for human monocyte-derived macrophages (MDM). MDM prepared by a conventional method markedly upregulate interferon-stimulated genes (ISGs) upon Mtb infection, while MDM prepared to better restrict Mtb do so much less. A mixture of antibodies inhibiting IFN-I signaling prevents ISG induction. Surprisingly, secreted IFN-I are undetectable until nearly two days after ISG induction. These same antibodies do not diminish Mtb-infected MDM death. MDM induce ISGs in response to picogram/mL levels of exogenous IFN-I while depleting similar quantities from the medium. Exogenous IFN-I increase the proportion of dead MDM. We speculate that Mtb-infected MDM produce and respond to minute levels of IFN-I, and that only some of the resultant signaling is susceptible to neutralizing antibodies. Many types of cells may secrete IFN-I in patients with TB, where IFN-I is likely to promote the death of infected macrophages.
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Affiliation(s)
- Angela M Lee
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
- Immunology & Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Carl F Nathan
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, NY, 10065, USA.
- Immunology & Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA.
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5
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Niu L, Wang H, Luo G, Zhou J, Hu Z, Yan B. Advances in understanding immune homeostasis in latent tuberculosis infection. WIREs Mech Dis 2024; 16:e1643. [PMID: 38351551 DOI: 10.1002/wsbm.1643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 07/13/2024]
Abstract
Nearly one-fourth of the global population is infected by Mycobacterium tuberculosis (Mtb), and approximately 90%-95% remain asymptomatic as latent tuberculosis infection (LTBI), an estimated 5%-10% of those with latent infections will eventually progress to active tuberculosis (ATB). Although it is widely accepted that LTBI transitioning to ATB results from a disruption of host immune balance and a weakening of protective immune responses, the exact underlying immunological mechanisms that promote this conversion are not well characterized. Thus, it is difficult to accurately predict tuberculosis (TB) progression in advance, leaving the LTBI population as a significant threat to TB prevention and control. This article systematically explores three aspects related to the immunoregulatory mechanisms and translational research about LTBI: (1) the distinct immunocytological characteristics of LTBI and ATB, (2) LTBI diagnostic markers discovery related to host anti-TB immunity and metabolic pathways, and (3) vaccine development focus on LTBI. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology Infectious Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Liangfei Niu
- Center for Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Hao Wang
- Center for Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Geyang Luo
- Center for Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Jing Zhou
- Department of Pathology, Center for Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Zhidong Hu
- Center for Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Bo Yan
- Center for Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
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Wu Z, Li M, Qu L, Zhang C, Xie W. Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary. MICROBIOME 2024; 12:115. [PMID: 38918820 PMCID: PMC11200988 DOI: 10.1186/s40168-024-01817-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 04/17/2024] [Indexed: 06/27/2024]
Abstract
BACKGROUND Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the "salt-in" strategy, involving inorganic ion uptake, or the "salt-out" strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem. RESULTS Here, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline-specific to low-, intermediate-, or high-salinity-based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the "inorganic ion transport and metabolism" COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the "salt-in" strategy, three to the "salt-out" strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K+ transporter related to the "salt-in" strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla. CONCLUSIONS We demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the "salt-in" strategy mediated by Trk-type K+ transporters for microorganisms thriving under osmotic stress in the short residence-time estuary. Video Abstract.
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Affiliation(s)
- Ziheng Wu
- School of Marine Sciences, Sun Yat-Sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Minchun Li
- School of Marine Sciences, Sun Yat-Sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Liping Qu
- School of Marine Sciences, Sun Yat-Sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-Sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China.
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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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Vu A, Glassman I, Campbell G, Yeganyan S, Nguyen J, Shin A, Venketaraman V. Host Cell Death and Modulation of Immune Response against Mycobacterium tuberculosis Infection. Int J Mol Sci 2024; 25:6255. [PMID: 38892443 PMCID: PMC11172987 DOI: 10.3390/ijms25116255] [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: 05/01/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), a prevalent infectious disease affecting populations worldwide. A classic trait of TB pathology is the formation of granulomas, which wall off the pathogen, via the innate and adaptive immune systems. Some key players involved include tumor necrosis factor-alpha (TNF-α), foamy macrophages, type I interferons (IFNs), and reactive oxygen species, which may also show overlap with cell death pathways. Additionally, host cell death is a primary method for combating and controlling Mtb within the body, a process which is influenced by both host and bacterial factors. These cell death modalities have distinct molecular mechanisms and pathways. Programmed cell death (PCD), encompassing apoptosis and autophagy, typically confers a protective response against Mtb by containing the bacteria within dead macrophages, facilitating their phagocytosis by uninfected or neighboring cells, whereas necrotic cell death benefits the pathogen, leading to the release of bacteria extracellularly. Apoptosis is triggered via intrinsic and extrinsic caspase-dependent pathways as well as caspase-independent pathways. Necrosis is induced via various pathways, including necroptosis, pyroptosis, and ferroptosis. Given the pivotal role of host cell death pathways in host defense against Mtb, therapeutic agents targeting cell death signaling have been investigated for TB treatment. This review provides an overview of the diverse mechanisms underlying Mtb-induced host cell death, examining their implications for host immunity. Furthermore, it discusses the potential of targeting host cell death pathways as therapeutic and preventive strategies against Mtb infection.
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Affiliation(s)
| | | | | | | | | | | | - Vishwanath Venketaraman
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (G.C.); (A.S.)
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9
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Nieto-Caballero VE, Reijneveld JF, Ruvalcaba A, Innocenzi G, Abeydeera N, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Budzik JM, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Suliman S, Gutierrez-Arcelus M. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. PLoS Genet 2024; 20:e1011313. [PMID: 38870230 PMCID: PMC11208071 DOI: 10.1371/journal.pgen.1011313] [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: 09/13/2023] [Revised: 06/26/2024] [Accepted: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
A quarter of humanity is estimated to have been exposed to Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n = 63) or did not progress to TB (controls, n = 63). Transcriptomic profiling of monocyte-derived DCs and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Four genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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Affiliation(s)
- Victor E. Nieto-Caballero
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Morelos, Mexico
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Josephine F. Reijneveld
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Angel Ruvalcaba
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Gabriel Innocenzi
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Nalin Abeydeera
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Samira Asgari
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kattya Lopez
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Sarah K. Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yang Luo
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Aparna Nathan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniela Fernandez-Salinas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marcos Chiñas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Segundo R. León
- Socios En Salud Sucursal Peru, Lima, Peru
- Medical Technology School and Global Health Research Institute, San Juan Bautista Private University, Lima, Perú
| | | | | | - Jonathan M. Budzik
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Soumya Raychaudhuri
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sara Suliman
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Gladstone-UCSF Institute of Genomic Immunology, University of California San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Initiative Biohub, San Francisco, California, United States of America
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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10
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Davies LRL, Wang C, Steigler P, Bowman KA, Fischinger S, Hatherill M, Fisher M, Mbandi SK, Rodo M, Ottenhoff THM, Dockrell HM, Sutherland JS, Mayanja-Kizza H, Boom WH, Walzl G, Kaufmann SHE, Nemes E, Scriba TJ, Lauffenburger D, Alter G, Fortune SM. Age and sex influence antibody profiles associated with tuberculosis progression. Nat Microbiol 2024; 9:1513-1525. [PMID: 38658786 PMCID: PMC11153143 DOI: 10.1038/s41564-024-01678-x] [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: 10/12/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Antibody features vary with tuberculosis (TB) disease state. Whether clinical variables, such as age or sex, influence associations between Mycobacterium tuberculosis-specific antibody responses and disease state is not well explored. Here we profiled Mycobacterium tuberculosis-specific antibody responses in 140 TB-exposed South African individuals from the Adolescent Cohort Study. We identified distinct response features in individuals progressing to active TB from non-progressing, matched controls. A multivariate antibody score differentially associated with progression (SeroScore) identified progressors up to 2 years before TB diagnosis, earlier than that achieved with the RISK6 transcriptional signature of progression. We validated these antibody response features in the Grand Challenges 6-74 cohort. Both the SeroScore and RISK6 correlated better with risk of TB progression in adolescents compared with adults, and in males compared with females. This suggests that age and sex are important, underappreciated modifiers of antibody responses associated with TB progression.
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Affiliation(s)
- Leela R L Davies
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Chuangqi Wang
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pia Steigler
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Kathryn A Bowman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michelle Fisher
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Miguel Rodo
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Hazel M Dockrell
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Jayne S Sutherland
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Harriet Mayanja-Kizza
- Department of Medicine and Department of Microbiology, Makerere University, Kampala, Uganda
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH, USA
| | - Gerhard Walzl
- Department of Science and Technology National Research Foundation 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
| | - Stefan H E Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
- Moderna Therapeutics, Cambridge, MA, USA.
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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11
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Krause R, Ogongo P, Tezera L, Ahmed M, Mbano I, Chambers M, Ngoepe A, Magnoumba M, Muema D, Karim F, Khan K, Lumamba K, Nargan K, Madansein R, Steyn A, Shalek AK, Elkington P, Leslie A. B cell heterogeneity in human tuberculosis highlights compartment-specific phenotype and functional roles. Commun Biol 2024; 7:584. [PMID: 38755239 PMCID: PMC11099031 DOI: 10.1038/s42003-024-06282-7] [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: 10/16/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
B cells are important in tuberculosis (TB) immunity, but their role in the human lung is understudied. Here, we characterize B cells from lung tissue and matched blood of patients with TB and found they are decreased in the blood and increased in the lungs, consistent with recruitment to infected tissue, where they are located in granuloma associated lymphoid tissue. Flow cytometry and transcriptomics identify multiple B cell populations in the lung, including those associated with tissue resident memory, germinal centers, antibody secretion, proinflammatory atypical B cells, and regulatory B cells, some of which are expanded in TB disease. Additionally, TB lungs contain high levels of Mtb-reactive antibodies, specifically IgM, which promotes Mtb phagocytosis. Overall, these data reveal the presence of functionally diverse B cell subsets in the lungs of patients with TB and suggest several potential localized roles that may represent a target for interventions to promote immunity or mitigate immunopathology.
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Affiliation(s)
- Robert Krause
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Paul Ogongo
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Liku Tezera
- National Institute for Health Research Southampton Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mohammed Ahmed
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ian Mbano
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mark Chambers
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Magalli Magnoumba
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel Muema
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Rajhmun Madansein
- Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Adrie Steyn
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for AIDS Research and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alex K Shalek
- Institute for Medical Engineering & Science, Department of Chemistry, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul Elkington
- National Institute for Health Research Southampton Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Al Leslie
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Division of Infection and Immunity, University College London, London, UK.
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12
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Lei H. Quantitative and Longitudinal Assessment of Systemic Innate Immunity in Health and Disease Using a 2D Gene Model. Biomedicines 2024; 12:969. [PMID: 38790931 PMCID: PMC11117654 DOI: 10.3390/biomedicines12050969] [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: 04/01/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Dysregulation of innate immunity is deeply involved in infectious and autoimmune diseases. For a better understanding of pathogenesis and improved management of these diseases, it is of vital importance to implement convenient monitoring of systemic innate immunity. Built upon our previous works on the host transcriptional response to infection in peripheral blood, we proposed a 2D gene model for the simultaneous assessment of two major components of systemic innate immunity, including VirSig as the signature of the host response to viral infection and BacSig as the signature of the host response to bacterial infection. The revelation of dysregulation in innate immunity by this 2D gene model was demonstrated with a wide variety of transcriptome datasets. In acute infection, distinctive patterns of VirSig and BacSig activation were observed in viral and bacterial infection. In comparison, both signatures were restricted to a defined range in the vast majority of healthy adults, regardless of age. In addition, BacSig showed significant elevation during pregnancy and an upward trend during development. In tuberculosis (TB), elevation of BacSig and VirSig was observed in a significant portion of active TB patients, and abnormal BacSig was also associated with a longer treatment course. In cystic fibrosis (CF), abnormal BacSig was observed in a subset of patients, and no overall change in BacSig abnormality was observed after the drug treatment. In systemic sclerosis-associated interstitial lung disease (SSc-ILD), significant elevation of VirSig and BacSig was observed in some patients, and treatment with a drug led to the further deviation of BacSig from the control level. In systemic lupus erythematosus (SLE), positivity for the anti-Ro autoantibody was associated with significant elevation of VirSig in SLE patients, and the additive effect of VirSig/BacSig activation was also observed in SLE patients during pregnancy. Overall, these data demonstrated that the 2D gene model can be used to assess systemic innate immunity in health and disease, with the potential clinical applications including patient stratification, prescription of antibiotics, understanding of pathogenesis, and longitudinal monitoring of treatment response.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; ; Tel.: +86-010-8409-7276
- Cunji Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
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13
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Bobba S, Chauhan KS, Akter S, Das S, Mittal E, Mathema B, Philips JA, Khader SA. A protective role for type I interferon signaling following infection with Mycobacterium tuberculosis carrying the rifampicin drug resistance-conferring RpoB mutation H445Y. PLoS Pathog 2024; 20:e1012137. [PMID: 38603763 PMCID: PMC11037539 DOI: 10.1371/journal.ppat.1012137] [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: 08/09/2023] [Revised: 04/23/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Interleukin-1 (IL-1) signaling is essential for controlling virulent Mycobacterium tuberculosis (Mtb) infection since antagonism of this pathway leads to exacerbated pathology and increased susceptibility. In contrast, the triggering of type I interferon (IFN) signaling is associated with the progression of tuberculosis (TB) disease and linked with negative regulation of IL-1 signaling. However, mice lacking IL-1 signaling can control Mtb infection if infected with an Mtb strain carrying the rifampin-resistance conferring mutation H445Y in its RNA polymerase β subunit (rpoB-H445Y Mtb). The mechanisms that govern protection in the absence of IL-1 signaling during rpoB-H445Y Mtb infection are unknown. In this study, we show that in the absence of IL-1 signaling, type I IFN signaling controls rpoB-H445Y Mtb replication, lung pathology, and excessive myeloid cell infiltration. Additionally, type I IFN is produced predominantly by monocytes and recruited macrophages and acts on LysM-expressing cells to drive protection through nitric oxide (NO) production to restrict intracellular rpoB-H445Y Mtb. These findings reveal an unexpected protective role for type I IFN signaling in compensating for deficiencies in IL-1 pathways during rpoB-H445Y Mtb infection.
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Affiliation(s)
- Suhas Bobba
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kuldeep S. Chauhan
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Sadia Akter
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Shibali Das
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ekansh Mittal
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, United States of America
| | - Jennifer A. Philips
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shabaana A. Khader
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
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14
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Kim JW, Nazareth J, Lee J, Patel H, Woltmann G, Verma R, O'Garra A, Haldar P. Interferon-gamma release assay conversion after Mycobacterium tuberculosis exposure specifically associates with greater risk of progression to tuberculosis: A prospective cohort study in Leicester, UK. Int J Infect Dis 2024; 141:106982. [PMID: 38408518 DOI: 10.1016/j.ijid.2024.02.025] [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: 09/21/2023] [Revised: 01/12/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024] Open
Abstract
OBJECTIVES We investigated whether quantifying the serial QuantiFERON-TB Gold (QFT) response improves tuberculosis (TB) risk stratification in pulmonary TB (PTB) contacts. METHODS A total of 297 untreated adult household PTB contacts, QFT tested at baseline and 3 months after index notification, were prospectively observed (median 1460 days). Normal variance of serial QFT responses was established in 46 extrapulmonary TB contacts. This informed categorisation of the response in QFT-positive PTB contacts as converters, persistently QFT-positive with significant increase (PPincrease), and without significant increase (PPno-increase). RESULTS In total, eight co-prevalent TB (disease ≤3 months after index notification) and 12 incident TB (>3 months after index notification) cases were diagnosed. Genetic linkage to the index strain was confirmed in all culture-positive progressors. The cumulative 2-year incident TB risk in QFT-positive contacts was 8.4% (95% confidence interval, 3.0-13.6%); stratifying by serial QFT response, significantly higher risk was observed in QFT converters (28%), compared with PPno-increase (4.8%) and PPincrease (3.7%). Converters were characterised by exposure to index cases with a shorter interval from symptom onset to diagnosis (median reduction 50.0 days, P = 0.013). CONCLUSIONS QFT conversion, rather than quantitative changes of a persistently positive serial QFT response, is associated with greater TB risk and exposure to rapidly progressive TB.
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Affiliation(s)
- Jee Whang Kim
- NIHR Leicester Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, UK; Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK.
| | - Joshua Nazareth
- NIHR Leicester Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, UK; Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Joanne Lee
- NIHR Leicester Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, UK; Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Hemu Patel
- Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Gerrit Woltmann
- NIHR Leicester Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, UK; Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Raman Verma
- NIHR Leicester Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, UK; Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Anne O'Garra
- Laboratory of Immunoregulation and Infection, Francis Crick Institute, London, UK; National Heart and Lung Institute, Imperial College, London, UK
| | - Pranabashis Haldar
- NIHR Leicester Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, UK; Department of Respiratory Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
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15
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Lai H, Lyu M, Ruan H, Liu Y, Liu T, Lei S, Xiao Y, Zhang S, Ying B. Large-scale analysis reveals splicing biomarkers for tuberculosis progression and prognosis. Comput Biol Med 2024; 171:108187. [PMID: 38402840 DOI: 10.1016/j.compbiomed.2024.108187] [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: 10/23/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Emerging evidence suggests that aberrant alternative splicing (AS) may play an important role in tuberculosis (TB). However, current knowledge regarding the value of AS in TB progression and prognosis remains unclear. METHOD Public RNA-seq datasets related to TB progression and prognosis were searched and AS analyses were conducted based on SUPPA2. Percent spliced in (PSI) was used for quantifying AS events and multiple machine learning (ML) methods were employed to construct predictive models. Area under curve (AUC), sensitivity and specificity were calculated to evaluate the model performance. RESULTS A total of 1587 samples from 7 datasets were included. Among 923 TB-progression related differential AS events (DASEs), 3 events (GET1-skipping exon (SE), TPD52-alternative first exons (AF) and TIMM10-alternative 5' splice site (A5)) were selected as candidate biomarkers; however, their predictive performance was limited. For TB prognosis, 5 events (PHF23-AF, KIF1B-SE, MACROD2-alternative 3' splice site (A3), CD55-retained intron (RI) and GALNT11-AF) were selected as candidates from the 1282 DASEs. Six ML methods were used to integrate these 5 events and XGBoost outperformed than others. AUC, sensitivity and specificity of XGBoost model were 0.875, 81.1% and 83.5% in training set, while they were 0.805, 68.4% and 73.2% in test set. CONCLUSION GET1-SE, TPD52-AF and TIMM10-A5 showed limited role in predicting TB progression, while PHF23-AF, KIF1B-SE, MACROD2-A3, CD55-RI and GALNT11-AF could well predict TB prognosis and work as candidate biomarkers. This work preliminarily explored the value of AS in predicting TB progression and prognosis and offered potential targets for further research.
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Affiliation(s)
- Hongli Lai
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Mengyuan Lyu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Hongxia Ruan
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Yang Liu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Tangyuheng Liu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Shuting Lei
- West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Yuling Xiao
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Shu Zhang
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Binwu Ying
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China.
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16
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Lee AM, Laurent P, Nathan CF, Barrat FJ. Neutrophil-plasmacytoid dendritic cell interaction leads to production of type I IFN in response to Mycobacterium tuberculosis. Eur J Immunol 2024; 54:e2350666. [PMID: 38161237 DOI: 10.1002/eji.202350666] [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: 07/13/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Mycobacterium tuberculosis (Mtb) can cause a latent infection that sometimes progresses to clinically active tuberculosis (TB). Type I interferons (IFN-I) have been implicated in initiating the progression from latency to active TB, in part because IFN-I stimulated genes are the earliest genes to be upregulated in patients as they advance to active TB. Plasmacytoid dendritic cells (pDCs) are major producers of IFN-I during viral infections and in response to autoimmune-induced neutrophil extracellular traps. pDCs have also been suggested to be the major producers of IFN-I during Mtb infection of mice and nonhuman primates, but direct evidence has been lacking. Here, we found that Mtb did not stimulate isolated human pDCs to produce IFN-I, but human neutrophils infected with Mtb-activated co-cultured pDCs to do so. Mtb-infected neutrophils produced neutrophil extracellular traps, whose exposed DNA is a well-known mechanism to activate pDCs to secrete IFN-I. We conclude that pDCs contribute to the IFN-I response during Mtb infection by interacting with infected neutrophils which may then promote Mtb pathogenesis.
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Affiliation(s)
- Angela M Lee
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
- Immunology & Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Paôline Laurent
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
- Hospital for Special Surgery, HSS Research Institute, New York, New York, USA
| | - Carl F Nathan
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
- Immunology & Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Franck J Barrat
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
- Immunology & Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
- Hospital for Special Surgery, HSS Research Institute, New York, New York, USA
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17
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Serene LG, Webber K, Champion PA, Schorey JS. Mycobacterium tuberculosis SecA2-dependent activation of host Rig-I/MAVs signaling is not conserved in Mycobacterium marinum. PLoS One 2024; 19:e0281564. [PMID: 38394154 PMCID: PMC10889897 DOI: 10.1371/journal.pone.0281564] [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: 02/06/2023] [Accepted: 11/02/2023] [Indexed: 02/25/2024] Open
Abstract
Retinoic acid inducible gene I (Rig-I) is a cytosolic pattern recognition receptor canonically described for its important role in sensing viral RNAs. Increasingly, bacterially-derived RNA from intracellular bacteria such as Mycobacterium tuberculosis, have been shown to activate the same host Rig-I/Mitochondrial antiviral sensing protein (MAVS) signaling pathway to drive a type-I interferon response that contributes to bacterial pathogenesis in vivo. In M. tuberculosis, this response is mediated by the protein secretion system SecA2, but little is known about whether this process is conserved in other pathogenic mycobacteria or the mechanism by which these nucleic acids gain access to the host cytoplasm. Because the M. tuberculosis and M. marinum SecA2 protein secretion systems share a high degree of genetic and functional conservation, we hypothesized that Rig-I/MAVS activation and subsequent induction of IFN-β secretion by host macrophages will also be conserved between these two mycobacterial species. To test this, we generated a ΔsecA2 M. marinum strain along with complementation strains expressing either the M. marinum or M. tuberculosis secA2 genes. Our results suggest that the ΔsecA2 strain has a growth defect in vitro but not in host macrophages. These intracellular growth curves also suggested that the calculation applied to estimate the number of bacteria added to macrophage monolayers in infection assays underestimates bacterial inputs for the ΔsecA2 strain. Therefore, to better examine secreted IFN-β levels when bacterial infection levels are equal across strains we plated bacterial CFUs at 2hpi alongside our ELISA based infections. This enabled us to normalize secreted levels of IFN-β to a standard number of bacteria. Applying this approach to both WT and MAVS-/- bone marrow derived macrophages we observed equal or higher levels of secreted IFN-β from macrophages infected with the ΔsecA2 M. marinum strain as compared to WT. Together our findings suggest that activation of host Rig-I/MAVS cytosolic sensors and subsequent induction of IFN-β response in a SecA2-dependent manner is not conserved in M. marinum under the conditions tested.
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Affiliation(s)
- Lindsay G. Serene
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Kylie Webber
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Jeffrey S. Schorey
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
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18
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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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19
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Ko ER, Reller ME, Tillekeratne LG, Bodinayake CK, Miller C, Burke TW, Henao R, McClain MT, Suchindran S, Nicholson B, Blatt A, Petzold E, Tsalik EL, Nagahawatte A, Devasiri V, Rubach MP, Maro VP, Lwezaula BF, Kodikara-Arachichi W, Kurukulasooriya R, De Silva AD, Clark DV, Schully KL, Madut D, Dumler JS, Kato C, Galloway R, Crump JA, Ginsburg GS, Minogue TD, Woods CW. Host-response transcriptional biomarkers accurately discriminate bacterial and viral infections of global relevance. Sci Rep 2023; 13:22554. [PMID: 38110534 PMCID: PMC10728077 DOI: 10.1038/s41598-023-49734-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Diagnostic limitations challenge management of clinically indistinguishable acute infectious illness globally. Gene expression classification models show great promise distinguishing causes of fever. We generated transcriptional data for a 294-participant (USA, Sri Lanka) discovery cohort with adjudicated viral or bacterial infections of diverse etiology or non-infectious disease mimics. We then derived and cross-validated gene expression classifiers including: 1) a single model to distinguish bacterial vs. viral (Global Fever-Bacterial/Viral [GF-B/V]) and 2) a two-model system to discriminate bacterial and viral in the context of noninfection (Global Fever-Bacterial/Viral/Non-infectious [GF-B/V/N]). We then translated to a multiplex RT-PCR assay and independent validation involved 101 participants (USA, Sri Lanka, Australia, Cambodia, Tanzania). The GF-B/V model discriminated bacterial from viral infection in the discovery cohort an area under the receiver operator curve (AUROC) of 0.93. Validation in an independent cohort demonstrated the GF-B/V model had an AUROC of 0.84 (95% CI 0.76-0.90) with overall accuracy of 81.6% (95% CI 72.7-88.5). Performance did not vary with age, demographics, or site. Host transcriptional response diagnostics distinguish bacterial and viral illness across global sites with diverse endemic pathogens.
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Affiliation(s)
- Emily R Ko
- Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Duke University Health System, Duke University School of Medicine, 3643 N. Roxboro St., Durham, NC, 27704, USA.
| | - Megan E Reller
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - L Gayani Tillekeratne
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Champica K Bodinayake
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Cameron Miller
- Clinical Research Unit, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Thomas W Burke
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ricardo Henao
- Department of Biostatistics and Informatics, Duke University, Durham, NC, USA
| | - Micah T McClain
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
| | - Sunil Suchindran
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Adam Blatt
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Elizabeth Petzold
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ephraim L Tsalik
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Danaher Diagnostics, Washington, DC, USA
| | - Ajith Nagahawatte
- Department of Microbiology, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Vasantha Devasiri
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Matthew P Rubach
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore, Singapore, Singapore
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
| | - Venance P Maro
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Bingileki F Lwezaula
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Maswenzi Regional Referral Hospital, Moshi, Tanzania
| | | | | | - Aruna D De Silva
- General Sir John Kotelawala Defence University, Colombo, Sri Lanka
| | - Danielle V Clark
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, MD, USA
| | - Kevin L Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, MD, USA
| | - Deng Madut
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - J Stephen Dumler
- Joint Departments of Pathology, School of Medicine, Uniformed Services University, Bethesda, MD, USA
| | - Cecilia Kato
- Centers for Disease Control and Prevention, National Center for Emerging Zoonotic Infectious Diseases, Atlanta, USA
| | - Renee Galloway
- Centers for Disease Control and Prevention, National Center for Emerging Zoonotic Infectious Diseases, Atlanta, USA
| | - John A Crump
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Geoffrey S Ginsburg
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- National Institute of Health, Bethesda, MD, USA
| | - Timothy D Minogue
- Diagnostic Systems Division, USAMRIID, Fort Detrick, Frederick, MD, USA
| | - Christopher W Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
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20
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Dang J, Shu J, Wang R, Yu H, Chen Z, Yan W, Zhao B, Ding L, Wang Y, Hu H, Li Z. The glycopatterns of Pseudomonas aeruginosa as a potential biomarker for its carbapenem resistance. Microbiol Spectr 2023; 11:e0200123. [PMID: 37861315 PMCID: PMC10714932 DOI: 10.1128/spectrum.02001-23] [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: 05/23/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE Bacterial surface glycans are an attractive therapeutic target in response to antibiotics; however, current knowledge of the corresponding mechanisms is rather limited. Antimicrobial susceptibility testing, genome sequencing, and MALDI-TOF MS, commonly used in recent years to analyze bacterial resistance, are unable to rapidly and efficiently establish associations between glycans and resistance. The discovery of new antimicrobial strategies still requires the introduction of promising analytical methods. In this study, we applied lectin microarray technology and a machine-learning model to screen for important glycan structures associated with carbapenem-resistant P. aeruginosa. This work highlights that specific glycopatterns can be important biomarkers associated with bacterial antibiotic resistance, which promises to provide a rapid entry point for exploring new resistance mechanisms in pathogens.
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Affiliation(s)
- Jing Dang
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jian Shu
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Ruiying Wang
- Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Hanjie Yu
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhuo Chen
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Wenbo Yan
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Bingxiang Zhao
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Li Ding
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Yuzi Wang
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Huizheng Hu
- Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Zheng Li
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
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21
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Phat NK, Tien NTN, Anh NK, Yen NTH, Lee YA, Trinh HKT, Le KM, Ahn S, Cho YS, Park S, Kim DH, Long NP, Shin JG. Alterations of lipid-related genes during anti-tuberculosis treatment: insights into host immune responses and potential transcriptional biomarkers. Front Immunol 2023; 14:1210372. [PMID: 38022579 PMCID: PMC10644770 DOI: 10.3389/fimmu.2023.1210372] [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: 04/22/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background The optimal diagnosis and treatment of tuberculosis (TB) are challenging due to underdiagnosis and inadequate treatment monitoring. Lipid-related genes are crucial components of the host immune response in TB. However, their dynamic expression and potential usefulness for monitoring response to anti-TB treatment are unclear. Methodology In the present study, we used a targeted, knowledge-based approach to investigate the expression of lipid-related genes during anti-TB treatment and their potential use as biomarkers of treatment response. Results and discussion The expression levels of 10 genes (ARPC5, ACSL4, PLD4, LIPA, CHMP2B, RAB5A, GABARAPL2, PLA2G4A, MBOAT2, and MBOAT1) were significantly altered during standard anti-TB treatment. We evaluated the potential usefulness of this 10-lipid-gene signature for TB diagnosis and treatment monitoring in various clinical scenarios across multiple populations. We also compared this signature with other transcriptomic signatures. The 10-lipid-gene signature could distinguish patients with TB from those with latent tuberculosis infection and non-TB controls (area under the receiver operating characteristic curve > 0.7 for most cases); it could also be useful for monitoring response to anti-TB treatment. Although the performance of the new signature was not better than that of previous signatures (i.e., RISK6, Sambarey10, Long10), our results suggest the usefulness of metabolism-centric biomarkers. Conclusions Lipid-related genes play significant roles in TB pathophysiology and host immune responses. Furthermore, transcriptomic signatures related to the immune response and lipid-related gene may be useful for TB diagnosis and treatment monitoring.
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Affiliation(s)
- Nguyen Ky Phat
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Tran Nam Tien
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Ky Anh
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Thi Hai Yen
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Yoon Ah Lee
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, Seoul, Republic of Korea
| | - Hoang Kim Tu Trinh
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh, Ho Chi Minh, Vietnam
| | - Kieu-Minh Le
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh, Ho Chi Minh, Vietnam
| | - Sangzin Ahn
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Seongoh Park
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, Seoul, Republic of Korea
- Data Science Center, Sungshin Women's University, Seoul, Republic of Korea
| | - Dong Hyun Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Jae-Gook Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
- Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
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22
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Mayer-Barber KD. Granulocytes subsets and their divergent functions in host resistance to Mycobacterium tuberculosis - a 'tipping-point' model of disease exacerbation. Curr Opin Immunol 2023; 84:102365. [PMID: 37437471 PMCID: PMC10543468 DOI: 10.1016/j.coi.2023.102365] [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: 04/01/2023] [Revised: 05/29/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Granulocytes are innate immune effector cells with essential functions in host resistance to bacterial infections. I will discuss emerging evidence that during Mycobacterium tuberculosis infection, counter-intuitively, eosinophils are host-protective while neutrophils are host detrimental. Additionally, I will propose a 'tipping-point' model in which neutrophils are an integral part of a feedforward loop driving tuberculosis disease exacerbation.
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Affiliation(s)
- Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, 20892, USA.
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23
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Kurtz SL, Rydén P, Elkins KL. Transcriptional signatures measured in whole blood correlate with protection against tuberculosis in inbred and outbred mice. PLoS One 2023; 18:e0289358. [PMID: 37535648 PMCID: PMC10399789 DOI: 10.1371/journal.pone.0289358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Abstract
Although BCG has been used for almost 100 years to immunize against Mycobacterium tuberculosis, TB remains a global public health threat. Numerous clinical trials are underway studying novel vaccine candidates and strategies to improve or replace BCG, but vaccine development still lacks a well-defined set of immune correlates to predict vaccine-induced protection against tuberculosis. This study aimed to address this gap by examining transcriptional responses to BCG vaccination in C57BL/6 inbred mice, coupled with protection studies using Diversity Outbred mice. We evaluated relative gene expression in blood obtained from vaccinated mice, because blood is easily accessible, and data can be translated to human studies. We first determined that the average peak time after vaccination is 14 days for gene expression of a small subset of immune-related genes in inbred mice. We then performed global transcriptomic analyses using whole blood samples obtained two weeks after mice were vaccinated with BCG. Using comparative bioinformatic analyses and qRT-PCR validation, we developed a working correlate panel of 18 genes that were highly correlated with administration of BCG but not heat-killed BCG. We then tested this gene panel using BCG-vaccinated Diversity Outbred mice and revealed associations between the expression of a subset of genes and disease outcomes after aerosol challenge with M. tuberculosis. These data therefore demonstrate that blood-based transcriptional immune correlates measured within a few weeks after vaccination can be derived to predict protection against M. tuberculosis, even in outbred populations.
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Affiliation(s)
- Sherry L Kurtz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
| | - Karen L Elkins
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
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24
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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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25
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Shaukat SN, Eugenin E, Nasir F, Khanani R, Kazmi SU. Identification of immune biomarkers in recent active pulmonary tuberculosis. Sci Rep 2023; 13:11481. [PMID: 37460564 DOI: 10.1038/s41598-023-38372-7] [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: 12/15/2022] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Tuberculosis (TB) has remained an unsolved problem and a major public health issue, particularly in developing countries. Pakistan is one of the countries with the highest tuberculosis infection rates globally. However, methods or biomarkers to detect early signs of TB infection are limited. Here, we characterized the mRNA profiles of immune responses in unstimulated Peripheral blood mononuclear cells obtained from treatment naïve patients with early signs of active pulmonary tuberculosis without previous history of clinical TB. We identified a unique mRNA profile in active TB compared to uninfected controls, including cytokines such as IL-27, IL-15, IL-2RA, IL-24, and TGFβ, transcription factors such as STAT1 and NFATC1 and immune markers/receptors such as TLR4, IRF1, CD80, CD28, and PTGDR2 from an overall 84 different transcripts analyzed. Among 12 significant differentially expressed transcripts, we identified five gene signatures which included three upregulated IL-27, STAT1, TLR4 and two downregulated IL-24 and CD80 that best discriminate between active pulmonary TB and uninfected controls with AUC ranging from 0.9 to 1. Our data identified a molecular immune signature associated with the early stages of active pulmonary tuberculosis and it could be further investigated as a potential biomarker of pulmonary TB.
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Affiliation(s)
- Sobia Naz Shaukat
- Immunology and Infectious Diseases Research Laboratory (IIDRL), Department of Microbiology, Karachi University, Karachi, Pakistan.
- Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan.
| | - Eliseo Eugenin
- Department of Neurobiology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Faizan Nasir
- Department of Immunology, Dadabhoy Institute of Higher Education, Karachi, Pakistan
| | - Rafiq Khanani
- Dow University of Health Sciences, Ojha Campus, Karachi, Pakistan
| | - Shahana Urooj Kazmi
- Immunology and Infectious Diseases Research Laboratory (IIDRL), Department of Microbiology, Karachi University, Karachi, Pakistan
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26
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Suliman S, Nieto-Caballero VE, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Gutierrez-Arcelus M. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.20.23291558. [PMID: 37425785 PMCID: PMC10327177 DOI: 10.1101/2023.06.20.23291558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
A quarter of humanity is estimated to be latently infected with Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n=63) or did not progress to TB (controls, n=63). Transcriptomic profiling of monocyte-derived dendritic cells (DCs) and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Five genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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Affiliation(s)
- Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Initiative Biohub, San Francisco, CA, USA
| | - Victor E. Nieto-Caballero
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Morelos 62210, Mexico
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samira Asgari
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kattya Lopez
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Sarah K. Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang Luo
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Aparna Nathan
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniela Fernandez-Salinas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcos Chiñas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Segundo R León
- Socios En Salud Sucursal Peru, Lima, Peru
- Medical Technology School and Global Health Research Institute, San Juan Bautista Private University, Lima, Perú
| | | | | | - Megan Murray
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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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: 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: 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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28
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Mundra A, Yegiazaryan A, Karsian H, Alsaigh D, Bonavida V, Frame M, May N, Gargaloyan A, Abnousian A, Venketaraman V. Pathogenicity of Type I Interferons in Mycobacterium tuberculosis. Int J Mol Sci 2023; 24:3919. [PMID: 36835324 PMCID: PMC9965986 DOI: 10.3390/ijms24043919] [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: 01/09/2023] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Tuberculosis (TB) is a leading cause of mortality due to infectious disease and rates have increased during the emergence of COVID-19, but many of the factors determining disease severity and progression remain unclear. Type I Interferons (IFNs) have diverse effector functions that regulate innate and adaptive immunity during infection with microorganisms. There is well-documented literature on type I IFNs providing host defense against viruses; however, in this review, we explore the growing body of work that indicates high levels of type I IFNs can have detrimental effects to a host fighting TB infection. We report findings that increased type I IFNs can affect alveolar macrophage and myeloid function, promote pathological neutrophil extracellular trap responses, inhibit production of protective prostaglandin 2, and promote cytosolic cyclic GMP synthase inflammation pathways, and discuss many other relevant findings.
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Affiliation(s)
- Akaash Mundra
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Aram Yegiazaryan
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Haig Karsian
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Dijla Alsaigh
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Victor Bonavida
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Mitchell Frame
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Nicole May
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Areg Gargaloyan
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Arbi Abnousian
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Vishwanath Venketaraman
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91768, USA
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29
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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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30
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Wallis RS, O'Garra A, Sher A, Wack A. Host-directed immunotherapy of viral and bacterial infections: past, present and future. Nat Rev Immunol 2023; 23:121-133. [PMID: 35672482 PMCID: PMC9171745 DOI: 10.1038/s41577-022-00734-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 02/06/2023]
Abstract
The advent of COVID-19 and the persistent threat of infectious diseases such as tuberculosis, malaria, influenza and HIV/AIDS remind us of the marked impact that infections continue to have on public health. Some of the most effective protective measures are vaccines but these have been difficult to develop for some of these infectious diseases even after decades of research. The development of drugs and immunotherapies acting directly against the pathogen can be equally challenging, and such pathogen-directed therapeutics have the potential disadvantage of selecting for resistance. An alternative approach is provided by host-directed therapies, which interfere with host cellular processes required for pathogen survival or replication, or target the host immune response to infection (immunotherapies) to either augment immunity or ameliorate immunopathology. Here, we provide a historical perspective of host-directed immunotherapeutic interventions for viral and bacterial infections and then focus on SARS-CoV-2 and Mycobacterium tuberculosis, two major human pathogens of the current era, to indicate the key lessons learned and discuss candidate immunotherapeutic approaches, with a focus on drugs currently in clinical trials.
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Affiliation(s)
- Robert S Wallis
- The Aurum Institute, Johannesburg, South Africa.
- Vanderbilt University, Nashville, TN, USA.
- Rutgers University, Newark, NJ, USA.
- Case Western Reserve University, Cleveland, OH, USA.
| | - Anne O'Garra
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, London, UK.
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31
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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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32
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Nick JA, Malcolm KC, Hisert KB, Wheeler EA, Rysavy NM, Poch K, Caceres S, Lovell VK, Armantrout E, Saavedra MT, Calhoun K, Chatterjee D, Aboellail I, De P, Martiniano SL, Jia F, Davidson RM. Culture independent markers of nontuberculous mycobacterial (NTM) lung infection and disease in the cystic fibrosis airway. Tuberculosis (Edinb) 2023; 138:102276. [PMID: 36417800 PMCID: PMC10965158 DOI: 10.1016/j.tube.2022.102276] [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: 10/15/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic pathogens that affect a relatively small but significant portion of the people with cystic fibrosis (CF), and may cause increased morbidity and mortality in this population. Cultures from the airway are the only test currently in clinical use for detecting NTM. Culture techniques used in clinical laboratories are insensitive and poorly suited for population screening or to follow progression of disease or treatment response. The lack of sensitive and quantitative markers of NTM in the airway impedes patient care and clinical trial design, and has limited our understanding of patterns of acquisition, latency and pathogenesis of disease. Culture-independent markers of NTM infection have the potential to overcome many of the limitations of standard NTM cultures, especially the very slow growth, inability to quantitate bacterial burden, and low sensitivity due to required decontamination procedures. A range of markers have been identified in sputum, saliva, breath, blood, urine, as well as radiographic studies. Proposed markers to detect presence of NTM or transition to NTM disease include bacterial cell wall products and DNA, as well as markers of host immune response such as immunoglobulins and the gene expression of circulating leukocytes. In all cases the sensitivity of culture-independent markers is greater than standard cultures; however, most do not discriminate between various NTM species. Thus, each marker may be best suited for a specific clinical application, or combined with other markers and traditional cultures to improve diagnosis and monitoring of treatment response.
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Affiliation(s)
- Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katherine B Hisert
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Emily A Wheeler
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Noel M Rysavy
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Silvia Caceres
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Valerie K Lovell
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Emily Armantrout
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Milene T Saavedra
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Kara Calhoun
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Ibrahim Aboellail
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Prithwiraj De
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Fan Jia
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
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33
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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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34
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Inflammation-mediated tissue damage in pulmonary tuberculosis and host-directed therapeutic strategies. Semin Immunol 2023; 65:101672. [PMID: 36469987 DOI: 10.1016/j.smim.2022.101672] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 12/04/2022]
Abstract
Treatment of tuberculosis (TB) involves the administration of anti-mycobacterial drugs for several months. The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb, the causative agent) together with increased disease severity in people with co-morbidities such as diabetes mellitus and HIV have hampered efforts to reduce case fatality. In severe disease, TB pathology is largely attributable to over-exuberant host immune responses targeted at controlling bacterial replication. Non-resolving inflammation driven by host pro-inflammatory mediators in response to high bacterial load leads to pulmonary pathology including cavitation and fibrosis. The need to improve clinical outcomes and reduce treatment times has led to a two-pronged approach involving the development of novel antimicrobials as well as host-directed therapies (HDT) that favourably modulate immune responses to Mtb. HDT strategies incorporate aspects of immune modulation aimed at downregulating non-productive inflammatory responses and augmenting antimicrobial effector mechanisms to minimise pulmonary pathology and accelerate symptom resolution. HDT in combination with existing antimycobacterial agents offers a potentially promising strategy to improve the long-term outcome for TB patients. In this review, we describe components of the host immune response that contribute to inflammation and tissue damage in pulmonary TB, including cytokines, matrix metalloproteinases, lipid mediators, and neutrophil extracellular traps. We then proceed to review HDT directed at these pathways.
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Rao AM, Popper SJ, Gupta S, Davong V, Vaidya K, Chanthongthip A, Dittrich S, Robinson MT, Vongsouvath M, Mayxay M, Nawtaisong P, Karmacharya B, Thair SA, Bogoch I, Sweeney TE, Newton PN, Andrews JR, Relman DA, Khatri P. A robust host-response-based signature distinguishes bacterial and viral infections across diverse global populations. Cell Rep Med 2022; 3:100842. [PMID: 36543117 PMCID: PMC9797950 DOI: 10.1016/j.xcrm.2022.100842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/12/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
Limited sensitivity and specificity of current diagnostics lead to the erroneous prescription of antibiotics. Host-response-based diagnostics could address these challenges. However, using 4,200 samples across 69 blood transcriptome datasets from 20 countries from patients with bacterial or viral infections representing a broad spectrum of biological, clinical, and technical heterogeneity, we show current host-response-based gene signatures have lower accuracy to distinguish intracellular bacterial infections from viral infections than extracellular bacterial infections. Using these 69 datasets, we identify an 8-gene signature to distinguish intracellular or extracellular bacterial infections from viral infections with an area under the receiver operating characteristic curve (AUROC) > 0.91 (85.9% specificity and 90.2% sensitivity). In prospective cohorts from Nepal and Laos, the 8-gene classifier distinguished bacterial infections from viral infections with an AUROC of 0.94 (87.9% specificity and 91% sensitivity). The 8-gene signature meets the target product profile proposed by the World Health Organization and others for distinguishing bacterial and viral infections.
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Affiliation(s)
- Aditya M. Rao
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Immunology Graduate Program, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen J. Popper
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Sanjana Gupta
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Krista Vaidya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Anisone Chanthongthip
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew T. Robinson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Pruksa Nawtaisong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Biraj Karmacharya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Simone A. Thair
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Isaac Bogoch
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David A. Relman
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA,Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA,Corresponding author
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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: 4] [Impact Index Per Article: 2.0] [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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Vestal BE, Wynn E, Moore CM. lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models. BMC Bioinformatics 2022; 23:489. [DOI: 10.1186/s12859-022-05019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
Studies that utilize RNA Sequencing (RNA-Seq) in conjunction with designs that introduce dependence between observations (e.g. longitudinal sampling) require specialized analysis tools to accommodate this additional complexity. This R package contains a set of utilities to fit linear mixed effects models to transformed RNA-Seq counts that properly account for this dependence when performing statistical analyses.
Results
In a simulation study comparing lmerSeq and two existing methodologies that also work with transformed RNA-Seq counts, we found that lmerSeq was comprehensively better in terms of nominal error rate control and statistical power.
Conclusions
Existing R packages for analyzing transformed RNA-Seq data with linear mixed models are limited in the variance structures they allow and/or the transformation methods they support. The lmerSeq package offers more flexibility in both of these areas and gave substantially better results in our simulations.
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Kaipilyawar V, Zhao Y, Wang X, Joseph NM, Knudsen S, Prakash Babu S, Muthaiah M, Hochberg NS, Sarkar S, Horsburgh CR, Ellner JJ, Johnson WE, Salgame P. Development and Validation of a Parsimonious Tuberculosis Gene Signature Using the digital NanoString nCounter Platform. Clin Infect Dis 2022; 75:1022-1030. [PMID: 35015839 PMCID: PMC9522394 DOI: 10.1093/cid/ciac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Blood-based biomarkers for diagnosing active tuberculosis (TB), monitoring treatment response, and predicting risk of progression to TB disease have been reported. However, validation of the biomarkers across multiple independent cohorts is scarce. A robust platform to validate TB biomarkers in different populations with clinical end points is essential to the development of a point-of-care clinical test. NanoString nCounter technology is an amplification-free digital detection platform that directly measures mRNA transcripts with high specificity. Here, we determined whether NanoString could serve as a platform for extensive validation of candidate TB biomarkers. METHODS The NanoString platform was used for performance evaluation of existing TB gene signatures in a cohort in which signatures were previously evaluated on an RNA-seq dataset. A NanoString codeset that probes 107 genes comprising 12 TB signatures and 6 housekeeping genes (NS-TB107) was developed and applied to total RNA derived from whole blood samples of TB patients and individuals with latent TB infection (LTBI) from South India. The TBSignatureProfiler tool was used to score samples for each signature. An ensemble of machine learning algorithms was used to derive a parsimonious biomarker. RESULTS Gene signatures present in NS-TB107 had statistically significant discriminative power for segregating TB from LTBI. Further analysis of the data yielded a NanoString 6-gene set (NANO6) that when tested on 10 published datasets was highly diagnostic for active TB. CONCLUSIONS The NanoString nCounter system provides a robust platform for validating existing TB biomarkers and deriving a parsimonious gene signature with enhanced diagnostic performance.
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Affiliation(s)
- Vaishnavi Kaipilyawar
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Yue Zhao
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xutao Wang
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Noyal M Joseph
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | | | - Senbagavalli Prakash Babu
- Department of Preventive and Social Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Muthuraj Muthaiah
- Department of Microbiology, State TB Training and Demonstration Center, Government Hospital for Chest Disease, Gorimedu, Puducherry, India
| | - Natasha S Hochberg
- Boston Medical Center, Boston, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Sonali Sarkar
- Department of Preventive and Social Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Charles R Horsburgh
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Jerrold J Ellner
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - W Evan Johnson
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
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39
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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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40
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Geng X, Wu X, Yang Q, Xin H, Zhang B, Wang D, Liu L, Liu S, Chen Q, Liu Z, Zhang M, Pan S, Zhang X, Gao L, Jin Q. Whole transcriptome sequencing reveals neutrophils’ transcriptional landscape associated with active tuberculosis. Front Immunol 2022; 13:954221. [PMID: 36059536 PMCID: PMC9436479 DOI: 10.3389/fimmu.2022.954221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Neutrophils have been recognized to play an important role in the pathogenesis of tuberculosis in recent years. Interferon-induced blood transcriptional signatures in ATB are predominantly driven by neutrophils. In this study, we performed global RNA-seq on peripheral blood neutrophils from active tuberculosis patients (ATB, n=15); latent tuberculosis infections (LTBI, n=22); and healthy controls (HC, n=21). The results showed that greater perturbations of gene expression patterns happened in neutrophils from ATB individuals than HC or those with LTBI, and a total of 344 differentially expressed genes (DEGs) were observed. Functional enrichment analysis showed that besides the interferon signaling pathway, multiple pattern recognition receptor pathways were significantly activated in ATB, such as NOD-like receptors and Toll-like receptors. Meanwhile, we also observed that the expression of genes related to endocytosis, secretory granules, and neutrophils degranulation were downregulated. Our data also showed that the NF-κB signaling pathway might be inhibited in patients with ATB, which could increase Mycobacterium tuberculosis survival and lead to active tuberculosis status. Furthermore, we validated the accuracy of some differentially expressed genes in an independent cohort using quantitative PCR, and obtained three novel genes (RBM3, CSRNP1, SRSF5) with the ability to discriminate active tuberculosis from LTBI and HC.
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Affiliation(s)
- Xingzhu Geng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaolin Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qianting Yang
- Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Key Laboratory of Infection & Immunity, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Henan Xin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Zhang
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Dakuan Wang
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Liguo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Song Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Chen
- Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Key Laboratory of Infection & Immunity, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Zisen Liu
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Mingxia Zhang
- Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Key Laboratory of Infection & Immunity, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Shouguo Pan
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Xiaobing Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Qi Jin, ; Xiaobing Zhang, ; Lei Gao,
| | - Lei Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Qi Jin, ; Xiaobing Zhang, ; Lei Gao,
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Qi Jin, ; Xiaobing Zhang, ; Lei Gao,
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Long NP, Anh NK, Yen NTH, Phat NK, Park S, Thu VTA, Cho YS, Shin JG, Oh JY, Kim DH. Comprehensive lipid and lipid-related gene investigations of host immune responses to characterize metabolism-centric biomarkers for pulmonary tuberculosis. Sci Rep 2022; 12:13395. [PMID: 35927287 PMCID: PMC9352691 DOI: 10.1038/s41598-022-17521-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
Despite remarkable success in the prevention and treatment of tuberculosis (TB), it remains one of the most devastating infectious diseases worldwide. Management of TB requires an efficient and timely diagnostic strategy. In this study, we comprehensively characterized the plasma lipidome of TB patients, then selected candidate lipid and lipid-related gene biomarkers using a data-driven, knowledge-based framework. Among 93 lipids that were identified as potential biomarker candidates, ether-linked phosphatidylcholine (PC O–) and phosphatidylcholine (PC) were generally upregulated, while free fatty acids and triglycerides with longer fatty acyl chains were downregulated in the TB group. Lipid-related gene enrichment analysis revealed significantly altered metabolic pathways (e.g., ether lipid, linolenic acid, and cholesterol) and immune response signaling pathways. Based on these potential biomarkers, TB patients could be differentiated from controls in the internal validation (random forest model, area under the curve [AUC] 0.936, 95% confidence interval [CI] 0.865–0.992). PC(O-40:4), PC(O-42:5), PC(36:0), and PC(34:4) were robust biomarkers able to distinguish TB patients from individuals with latent infection and healthy controls, as shown in the external validation. Small changes in expression were identified for 162 significant lipid-related genes in the comparison of TB patients vs. controls; in the random forest model, their utilities were demonstrated by AUCs that ranged from 0.829 to 0.956 in three cohorts. In conclusion, this study introduced a potential framework that can be used to identify and validate metabolism-centric biomarkers.
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Affiliation(s)
- Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Ky Anh
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Thi Hai Yen
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Ky Phat
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Seongoh Park
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, Seoul, Republic of Korea
| | - Vo Thuy Anh Thu
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Jae-Gook Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea.,Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - Jee Youn Oh
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Republic of Korea.
| | - Dong Hyun Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea.
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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: 0] [Impact Index Per Article: 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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43
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Akter S, Chauhan KS, Dunlap MD, Choreño-Parra JA, Lu L, Esaulova E, Zúñiga J, Artyomov MN, Kaushal D, Khader SA. Mycobacterium tuberculosis infection drives a type I IFN signature in lung lymphocytes. Cell Rep 2022; 39:110983. [PMID: 35732116 PMCID: PMC9616001 DOI: 10.1016/j.celrep.2022.110983] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/20/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) infects 25% of the world's population and causes tuberculosis (TB), which is a leading cause of death globally. A clear understanding of the dynamics of immune response at the cellular level is crucial to design better strategies to control TB. We use the single-cell RNA sequencing approach on lung lymphocytes derived from healthy and Mtb-infected mice. Our results show the enrichment of the type I IFN signature among the lymphoid cell clusters, as well as heat shock responses in natural killer (NK) cells from Mtb-infected mice lungs. We identify Ly6A as a lymphoid cell activation marker and validate its upregulation in activated lymphoid cells following infection. The cross-analysis of the type I IFN signature in human TB-infected peripheral blood samples further validates our results. These findings contribute toward understanding and characterizing the transcriptional parameters at a single-cell depth in a highly relevant and reproducible mouse model of TB.
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Affiliation(s)
- Sadia Akter
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA,These authors contributed equally
| | - Kuldeep S. Chauhan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA,These authors contributed equally
| | - Micah D. Dunlap
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - José Alberto Choreño-Parra
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA,Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas,” Mexico City 14080, Mexico,Laboratorio de Inmunoquímica I, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 07320, Mexico
| | - Lan Lu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joaquin Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas,” Mexico City 14080, Mexico,Laboratorio de Inmunoquímica I, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 07320, Mexico
| | - Maxim N. Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.
| | - Shabaana A. Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA,Lead contact,Correspondence: (D.K.), (S.A.K.) https://doi.org/10.1016/j.celrep.2022.110983
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44
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Sheerin D, Abhimanyu, Peton N, Vo W, Allison CC, Wang X, Johnson WE, Coussens AK. Immunopathogenic overlap between COVID-19 and tuberculosis identified from transcriptomic meta-analysis and human macrophage infection. iScience 2022; 25:104464. [PMID: 35634577 PMCID: PMC9130411 DOI: 10.1016/j.isci.2022.104464] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 01/14/2022] [Accepted: 05/18/2022] [Indexed: 12/25/2022] Open
Abstract
Current and previous tuberculosis (TB) increase the risk of COVID-19 mortality and severe disease. To identify mechanisms of immunopathogenic interaction between COVID-19 and TB, we performed a systematic review and patient-level meta-analysis of COVID-19 transcriptomic signatures, spanning disease severity, from whole blood, PBMCs, and BALF. 35 eligible signatures were profiled on 1181 RNA-seq samples from 853 individuals across the spectrum of TB infection. Thirteen COVID-19 gene-signatures had significantly higher "COVID-19 risk scores" in active TB and latent TB progressors compared with non-progressors and uninfected controls (p<0·005), in three independent cohorts. Integrative single-cell-RNAseq analysis identified FCN1- and SPP1-expressing macrophages enriched in severe COVID-19 BALF and active TB blood. Gene ontology and protein-protein interaction networks identified 12-gene disease-exacerbation hot spots between COVID-19 and TB. Finally, we in vitro validated that SARS-CoV-2 infection is increased in human macrophages cultured in the inflammatory milieu of Mtb-infected macrophages, correlating with TMPRSS2, IFNA1, IFNB1, IFNG, TNF, and IL1B induction.
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Affiliation(s)
- Dylan Sheerin
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville 3279, VIC, Australia
| | - Abhimanyu
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Observatory, 7925 Western Cape, South Africa
| | - Nashied Peton
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville 3279, VIC, Australia
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Observatory, 7925 Western Cape, South Africa
| | - William Vo
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville 3279, VIC, Australia
| | - Cody Charles Allison
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville 3279, VIC, Australia
| | - Xutao Wang
- Division of Computational Biomedicine and Department of Biostatistics, Boston University, Boston, MA 02118, USA
| | - W. Evan Johnson
- Division of Computational Biomedicine and Department of Biostatistics, Boston University, Boston, MA 02118, USA
| | - Anna Kathleen Coussens
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville 3279, VIC, Australia
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Observatory, 7925 Western Cape, South Africa
- Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia
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45
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Kang TG, Kwon KW, Kim K, Lee I, Kim MJ, Ha SJ, Shin SJ. Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx. Nat Commun 2022; 13:3155. [PMID: 35672321 PMCID: PMC9174268 DOI: 10.1038/s41467-022-30914-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 05/06/2022] [Indexed: 01/09/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is often exacerbated upon coinfection, but the underlying immunological mechanisms remain unclear. Here, to elucidate these mechanisms, we use an Mtb and lymphocytic choriomeningitis virus coinfection model. Viral coinfection significantly suppresses Mtb-specific IFN-γ production, with elevated bacterial loads and hyperinflammation in the lungs. Type I IFN signaling blockade rescues the Mtb-specific IFN-γ response and ameliorates lung immunopathology. Single-cell sequencing, tissue immunofluorescence staining, and adoptive transfer experiments indicate that viral infection-induced type I IFN signaling could inhibit CXCL9/10 production in myeloid cells, ultimately impairing pulmonary migration of Mtb-specific CD4+ T cells. Thus, our study suggests that augmented and sustained type I IFNs by virus coinfection prior to the pulmonary localization of Mtb-specific Th1 cells exacerbates TB immunopathogenesis by impeding the Mtb-specific Th1 cell influx. Our study highlights a negative function of viral coinfection-induced type I IFN responses in delaying Mtb-specific Th1 responses in the lung. Viral coinfection alongside mycobacterium tuberculosis (Mtb) infection may lead to immune complications or interference with immune responses. Here the authors show that in mice infected with Mtb and LCMV virus the specific TH1 response to MTb is reduced through a type I IFN response to the infecting virus.
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Affiliation(s)
- Tae Gun Kang
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.,Brain Korea 21 (BK21) FOUR Program, Yonsei Education & Research Center for Biosystems, Yonsei University, Seoul, 03722, Republic of Korea
| | - Kee Woong Kwon
- Department of Microbiology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kyungsoo Kim
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.,Institute for Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Myeong Joon Kim
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.,Brain Korea 21 (BK21) FOUR Program, Yonsei Education & Research Center for Biosystems, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea. .,Brain Korea 21 (BK21) FOUR Program, Yonsei Education & Research Center for Biosystems, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Sung Jae Shin
- Department of Microbiology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea. .,Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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46
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Wynn EA, Vestal BE, Fingerlin TE, Moore CM. A comparison of methods for multiple degree of freedom testing in repeated measures RNA-sequencing experiments. BMC Med Res Methodol 2022; 22:153. [PMID: 35643435 PMCID: PMC9148455 DOI: 10.1186/s12874-022-01615-8] [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: 02/15/2022] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background As the cost of RNA-sequencing decreases, complex study designs, including paired, longitudinal, and other correlated designs, become increasingly feasible. These studies often include multiple hypotheses and thus multiple degree of freedom tests, or tests that evaluate multiple hypotheses jointly, are often useful for filtering the gene list to a set of interesting features for further exploration while controlling the false discovery rate. Though there are several methods which have been proposed for analyzing correlated RNA-sequencing data, there has been little research evaluating and comparing the performance of multiple degree of freedom tests across methods. Methods We evaluated 11 different methods for modelling correlated RNA-sequencing data by performing a simulation study to compare the false discovery rate, power, and model convergence rate across several hypothesis tests and sample size scenarios. We also applied each method to a real longitudinal RNA-sequencing dataset. Results Linear mixed modelling using transformed data had the best false discovery rate control while maintaining relatively high power. However, this method had high model non-convergence, particularly at small sample sizes. No method had high power at the lowest sample size. We found a mix of conservative and anti-conservative behavior across the other methods, which was influenced by the sample size and the hypothesis being evaluated. The patterns observed in the simulation study were largely replicated in the analysis of a longitudinal study including data from intensive care unit patients experiencing cardiogenic or septic shock. Conclusions Multiple degree of freedom testing is a valuable tool in longitudinal and other correlated RNA-sequencing experiments. Of the methods that we investigated, linear mixed modelling had the best overall combination of power and false discovery rate control. Other methods may also be appropriate in some scenarios. Supplementary Information The online version contains supplementary material available at (10.1186/s12874-022-01615-8).
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47
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Khan A, Zhang K, Singh VK, Mishra A, Kachroo P, Bing T, Won JH, Mani A, Papanna R, Mann LK, Ledezma-Campos E, Aguillon-Duran G, Canaday DH, David SA, Restrepo BI, Viet NN, Phan H, Graviss EA, Musser JM, Kaushal D, Gauduin MC, Jagannath C. Human M1 macrophages express unique innate immune response genes after mycobacterial infection to defend against tuberculosis. Commun Biol 2022; 5:480. [PMID: 35590096 PMCID: PMC9119986 DOI: 10.1038/s42003-022-03387-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/21/2022] [Indexed: 12/23/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is responsible for approximately 1.5 million deaths each year. Though 10% of patients develop tuberculosis (TB) after infection, 90% of these infections are latent. Further, mice are nearly uniformly susceptible to Mtb but their M1-polarized macrophages (M1-MΦs) can inhibit Mtb in vitro, suggesting that M1-MΦs may be able to regulate anti-TB immunity. We sought to determine whether human MΦ heterogeneity contributes to TB immunity. Here we show that IFN-γ-programmed M1-MΦs degrade Mtb through increased expression of innate immunity regulatory genes (Inregs). In contrast, IL-4-programmed M2-polarized MΦs (M2-MΦs) are permissive for Mtb proliferation and exhibit reduced Inregs expression. M1-MΦs and M2-MΦs express pro- and anti-inflammatory cytokine-chemokines, respectively, and M1-MΦs show nitric oxide and autophagy-dependent degradation of Mtb, leading to increased antigen presentation to T cells through an ATG-RAB7-cathepsin pathway. Despite Mtb infection, M1-MΦs show increased histone acetylation at the ATG5 promoter and pro-autophagy phenotypes, while increased histone deacetylases lead to decreased autophagy in M2-MΦs. Finally, Mtb-infected neonatal macaques express human Inregs in their lymph nodes and macrophages, suggesting that M1 and M2 phenotypes can mediate immunity to TB in both humans and macaques. We conclude that human MФ subsets show unique patterns of gene expression that enable differential control of TB after infection. These genes could serve as targets for diagnosis and immunotherapy of TB.
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Affiliation(s)
- Arshad Khan
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vipul K Singh
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Abhishek Mishra
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Priyanka Kachroo
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Tian Bing
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jong Hak Won
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHSC, Houston, TX, USA
| | - Arunmani Mani
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHSC, Houston, TX, USA
| | - Ramesha Papanna
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHSC, Houston, TX, USA
| | - Lovepreet K Mann
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHSC, Houston, TX, USA
| | | | | | - David H Canaday
- Division of Infectious Disease, Case Western Reserve University Cleveland VA, Cleveland, OH, USA
| | - Sunil A David
- Virovax, LLC, Adjuvant Division, Lawrence, Kansas, USA
| | - Blanca I Restrepo
- UT School of Public Health, Brownsville, and STDOI, UT Rio Grande Valley, Brownsville, TX, USA
| | | | - Ha Phan
- Center for Promotion of Advancement of Society, Ha Noi, Vietnam
| | - Edward A Graviss
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Marie Claire Gauduin
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA.
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48
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Gilbertson SE, Walter HC, Gardner K, Wren SN, Vahedi G, Weinmann AS. Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans. Cell Rep 2022; 39:110769. [PMID: 35508135 PMCID: PMC9142060 DOI: 10.1016/j.celrep.2022.110769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 12/11/2022] Open
Abstract
Distinguishing between conserved and divergent regulatory mechanisms is
essential for translating preclinical research from mice to humans, yet there is
a lack of information about how evolutionary genome rearrangements affect the
regulation of the immune response, a rapidly evolving system. The current model
is topologically associating domains (TADs) are conserved between species,
buffering evolutionary rearrangements and conserving long-range interactions
within a TAD. However, we find that TADs frequently span evolutionary
translocation and inversion breakpoints near genes with species-specific
expression in immune cells, creating unique enhancer-promoter interactions
exclusive to the mouse or human genomes. This includes TADs encompassing
immune-related transcription factors, cytokines, and receptors. For example, we
uncover an evolutionary rearrangement that created a shared LPS-inducible
regulatory module between OASL and P2RX7 in
human macrophages that is absent in mice. Therefore, evolutionary genome
rearrangements disrupt TAD boundaries, enabling sequence-conserved enhancer
elements from divergent genomic locations between species to create unique
regulatory modules. It is currently unclear how evolutionary genome rearrangements affecting
the mouse and human genomes influence the expression of genes important in
immunity. Gilbertson et al. report that evolutionary genome rearrangements
disrupt topologically associating domain boundaries, enabling sequence-conserved
enhancer elements from divergent locations between species to create unique
regulatory modules.
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Affiliation(s)
- Sarah E Gilbertson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hannah C Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Katherine Gardner
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Spencer N Wren
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Golnaz Vahedi
- Department of Genetics, Institute of Immunology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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49
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Chedid C, Andrieu T, Kokhreidze E, Tukvadze N, Biswas S, Ather MF, Uddin MKM, Banu S, De Maio F, Delogu G, Endtz H, Goletti D, Vocanson M, Dumitrescu O, Hoffmann J, Ader F. In-Depth Immunophenotyping With Mass Cytometry During TB Treatment Reveals New T-Cell Subsets Associated With Culture Conversion. Front Immunol 2022; 13:853572. [PMID: 35392094 PMCID: PMC8980213 DOI: 10.3389/fimmu.2022.853572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/22/2022] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is a difficult-to-treat infection because of multidrug regimen requirements based on drug susceptibility profiles and treatment observance issues. TB cure is defined by mycobacterial sterilization, technically complex to systematically assess. We hypothesized that microbiological outcome was associated with stage-specific immune changes in peripheral whole blood during TB treatment. The T-cell phenotypes of treated TB patients were prospectively characterized in a blinded fashion using mass cytometry after Mycobacterium tuberculosis (Mtb) antigen stimulation with QuantiFERON-TB Gold Plus, and then correlated to sputum culture status. At two months of treatment, cytotoxic and terminally differentiated CD8+ T-cells were under-represented and naïve CD4+ T-cells were over-represented in positive- versus negative-sputum culture patients, regardless of Mtb drug susceptibility. At treatment completion, a T-cell immune shift towards differentiated subpopulations was associated with TB cure. Overall, we identified specific T-cell profiles associated with slow sputum converters, which brings new insights in TB prognostic biomarker research designed for clinical application.
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Affiliation(s)
- Carole Chedid
- Centre International de Recherche en Infectiologie, Legionella Pathogenesis Group, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, École Normale Supérieure de Lyon, Lyon, France.,Medical and Scientific Department, Fondation Mérieux, Lyon, France.,Département de Biologie, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Thibault Andrieu
- Cytometry Core Facility, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Eka Kokhreidze
- National Center for Tuberculosis and Lung Diseases (NCTBLD), Tbilisi, Georgia
| | - Nestani Tukvadze
- National Center for Tuberculosis and Lung Diseases (NCTBLD), Tbilisi, Georgia
| | - Samanta Biswas
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md Fahim Ather
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Khaja Mafij Uddin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sayera Banu
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Flavio De Maio
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Delogu
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Hubert Endtz
- Medical and Scientific Department, Fondation Mérieux, Lyon, France
| | - Delia Goletti
- Department of Epidemiology and Preclinical Research, "L. Spallanzani" National Institute for Infectious Diseases-IRCCS, Rome, Italy
| | - Marc Vocanson
- Centre International de Recherche en Infectiologie, Legionella Pathogenesis Group, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Oana Dumitrescu
- Centre International de Recherche en Infectiologie, Legionella Pathogenesis Group, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, École Normale Supérieure de Lyon, Lyon, France.,Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Lyon, France.,Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
| | - Jonathan Hoffmann
- Centre International de Recherche en Infectiologie, Legionella Pathogenesis Group, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, École Normale Supérieure de Lyon, Lyon, France.,Medical and Scientific Department, Fondation Mérieux, Lyon, France
| | - Florence Ader
- Centre International de Recherche en Infectiologie, Legionella Pathogenesis Group, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, École Normale Supérieure de Lyon, Lyon, France.,Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Département des Maladies Infectieuses et Tropicales, Lyon, France
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50
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Zhang XJ, Xu HS, Li CH, Fu YR, Yi ZJ. Up-regulated SAMD9L modulated by TLR2 and HIF-1α as a promising biomarker in tuberculosis. J Cell Mol Med 2022; 26:2935-2946. [PMID: 35388602 PMCID: PMC9097843 DOI: 10.1111/jcmm.17307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 02/10/2022] [Accepted: 03/08/2022] [Indexed: 11/29/2022] Open
Abstract
The aim of this study was to identify potential biomarkers of TB in blood and determine their function in Mtb-infected macrophages. First of all, WGCNA was used to analyse 9451 genes with significant changes in TB patients' whole blood. The 220 interferon-γ-related genes were identified, and then 30 key genes were screened using Cytoscape. Then, the AUC values of key genes were calculated to further narrow the gene range. Finally, we identified 9 genes from GSE19444. ROC analysis showed that SAMD9L, among 9 genes, had a high diagnostic value (AUC = 0.925) and a differential diagnostic value (AUC>0.865). To further narrow down the range of DEGs, the top 10 hub-connecting genes were screened from monocytes (GSE19443). Finally, we obtained 4 genes (SAMD9L, GBP1, GBP5 and STAT1) by intersections of genes from monocytes and whole blood. Among them, it was found that the function of SAMD9L was unknown after data review, so this paper studied this gene. Our results showed that SAMD9L is up-regulated and suppresses cell necrosis, and might be regulated by TLR2 and HIF-1α during Mtb infection. In addition, miR-181b-5p is significantly up-regulated in the peripheral blood plasma of tuberculosis patients, which has a high diagnostic value (AUC = 0.969).
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Affiliation(s)
- Xiang-Juan Zhang
- Department of Pathogen Biology, School of Basic Medicine, Weifang Medical University, Weifang, China.,School of Medical Laboratory, Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Weifang Medical University, Weifang, China
| | - Hai-Shan Xu
- School of Medical Laboratory, Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Weifang Medical University, Weifang, China
| | - Chong-Hui Li
- School of Medical Laboratory, Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Weifang Medical University, Weifang, China
| | - Yu-Rong Fu
- Department of Pathogen Biology, School of Basic Medicine, Weifang Medical University, Weifang, China.,School of Medical Laboratory, Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Weifang Medical University, Weifang, China
| | - Zheng-Jun Yi
- School of Medical Laboratory, Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Weifang Medical University, Weifang, China
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