Active Tuberculosis, Bacterial Infections, Gene Expression, Gene Expression Profiling, Infection, Viral Diseases
Conditions
Keywords
host response, transcriptome, Single cell-type gene expression, triage, fever, febrile patients
Brief summary
Febrile illness is a common condition, particularly among young patients and it is crucial to have an early triage of patients according to various aetiologies to enable appropriate treatment. Most diagnostic tests are targeted towards the detection of pathogens while other assays are mostly related to serum proteins. Blood cells transcriptome has been explored to differentiate bacterial and viral infections. Here, we propose to develop a rapid test using the host responses in terms of gene expressions of single-cell populations of peripheral leukocytes (monocytes and granulocytes) to differentiate three major categories of infections that are bacterial, viral, and tuberculosis. The assay is called Direct leukocyte single cell-type transcript abundance (TA) assay (DIRECT LS-TA) as it can directly determine the gene expression of a specified single cell-type (e.g. monocytes and granulocytes) among various leukocyte cell populations directly in a peripheral blood sample. Such results signify the nature of host response and can be used to indicate the type of infection (viral, bacterial or active tuberculosis).
Detailed description
DIRECT LS-TA is a ratio-based biomarker (RBB) for blood gene expression analysis which can be performed in commonly available equipments (e.g. qPCR or digital PCR machines). Using the ratio of TA of prior defined numerator gene and denominator gene, this RBB can quantify gene expression of the specified constitutional single cell-type (e.g. monocytes and granulocytes) inside a cell-mixture sample of Whole blood. DIRECT LS-TA was a method pioneered by the PI \[Tang 2017, https://patents.google.com/patent/US9589099B2/\]. And it has been developed for quantification of early B cell response after vaccination \[DOI: 10.3390/genes12070971\]. Recently, the method is used to develop host response biomarkers after infection to differentiate the type of pathogens (such as viral, bacterial or active tuberculosis). Numerator and denominator genes have been identified by using public gene expression datasets for monocytes and granulocytes. Diagnostic performance was good using these public data. Therefore, these RBBs will be applied in these retrospective samples to evaluate and compare their diagnostic (triage) performance of febrile patients into different pathogen etiologies.
Interventions
OTHERNo intervention
No intervention for this retrospective study
Sponsors
Chinese University of Hong Kong
Study design
Observational model
CASE_CONTROL
Time perspective
RETROSPECTIVE
Eligibility
Sex/Gender
ALL
Age
18 Years to No maximum
Healthy volunteers
Yes
Inclusion criteria
* Bacterial infection sample: positive isolation of organism in blood culture (Bacterial infection sample group) * Clinical diagnosed active TB (Tuberculosis infection group)
Exclusion criteria
* End stage renal failure * Pregnancy * Infections for which long term antibiotic treatment is strongly recommended (including infective endocarditis, osteoarticular infections, cerebral or hepatic or lung abscesses, tuberculosis or nontuberculous mycobacterial infections)
Design outcomes
Primary
| Measure | Time frame | Description |
|---|---|---|
| Bacterial infection host response Direct LS-TA in monocytes (pro-inflammatory response) | 1 day (first collected sample after admission) | Direct LS-TA is a kind of RBB that can be readily quantified by qPCR or dPCR of a pair of genes, the RBB numerator gene and the RBB denominator gene. The biomarker is the ratio of the 2 genes. Single cell-type: Monocyte. RBB numerator gene: VNN1, or NLRC4. RBB denominator gene: PSAP, CTSS or CPVL. The various RBBs will be compared in terms of their sensitivity/specificity of diagnostic performance in the vaccination control samples and samples from infection groups. AUC of ROC analysis will be performed where appropriate. |
| Viral host response Direct LS-TA in monocytes (Type I interferon response) | 1 day (first collected sample after admission) | Direct LS-TA is a kind of RBB that can be readily quantified by qPCR or dPCR of a pair of genes, the RBB numerator gene and the RBB denominator gene. The biomarker is the ratio of the 2 genes. Single cell-type: Monocyte. RBB numerator gene: IFI27 or IFI44L. RBB denominator gene: PSAP, CTSS or CPVL. The various RBB (e.g. IFI27/PSAP and IFI44L/PSAP ratios) will be compared in terms of their sensitivity/specificity of diagnostic performance in the vaccination control samples and samples from infection groups. AUC of ROC analysis will be performed where appropriate. |
| Viral host response Direct LS-TA in granulocytes (Type I interferon response) | 1 day (first collected sample after admission) | Direct LS-TA is a kind of RBB that can be readily quantified by qPCR or dPCR of a pair of genes, the RBB numerator gene and the RBB denominator gene. The biomarker is the ratio of the 2 genes. Single cell-type: Granulocyte. RBB numerator gene: RSAD2 or IFIT1. RBB denominator gene: SAT1 or SRGN. The various RBB will be compared in terms of their sensitivity/specificity of diagnostic performance in the vaccination control samples and samples from infection groups. AUC of ROC analysis will be performed where appropriate. |
| Active TB host response Direct LS-TA in granulocytes (Type II interferon response) | 1 day (first collected sample after admission) | Direct LS-TA is a kind of RBB that can be readily quantified by qPCR or dPCR of a pair of genes, the RBB numerator gene and the RBB denominator gene. The biomarker is the ratio of the 2 genes. Single cell-type: granulocyte. RBB numerator gene: ANKRD22, BATF2, CD274, FCGR1A or ETV7. RBB denominator gene: SAT1 or SRGN. The various RBB will be compared in terms of their sensitivity/specificity of diagnostic performance in the vaccination control samples and samples from infection groups. AUC of ROC analysis will be performed where appropriate. |
| Bacterial infection host response Direct LS-TA in granulocytes (pro-inflammatory response) | 1 day (first collected sample after admission) | Direct LS-TA is a kind of RBB that can be readily quantified by qPCR or dPCR of a pair of genes, the RBB numerator gene and the RBB denominator gene. The biomarker is the ratio of the 2 genes. Single cell-type: Granulocyte. RBB numerator gene: ALPL, ARG1, or ANXA3. RBB denominator gene: SAT1 or SRGN. The various RBB will be compared in terms of their sensitivity/specificity of diagnostic performance in the vaccination control samples and samples from infection groups. AUC of ROC analysis will be performed where appropriate. |
| Active TB host response Direct LS-TA in monocytes (Type II interferon response) | 1 day (first collected sample after admission) | Direct LS-TA is a kind of RBB that can be readily quantified by qPCR or dPCR of a pair of genes, the RBB numerator gene and the RBB denominator gene. The biomarker is the ratio of the 2 genes. Single cell-type: Monocyte. RBB numerator gene: WARS1, ATF3 or CALHM6. RBB denominator gene: PSAP, CTSS or CPVL. The various RBB will be compared in terms of their sensitivity/specificity of diagnostic performance in the vaccination control samples and samples from infection groups. AUC of ROC analysis will be performed where appropriate. |
Secondary
| Measure | Time frame | Description |
|---|---|---|
| Reference intervals and median of these DIRECT LS-TA RBB in the control group | 1 day (first collected sample after admission) | The median value and the central 95% range of each RBB will be determined. |
Countries
Hong Kong
Outcome results
None listed