Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
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).
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.
Not provided
Not provided
Not provided
Not provided
Not provided
| Label | Type | Description | Intervention Names |
|---|---|---|---|
| Vaccination Controls | Up to 200 adult samples collected as the baseline of this study will be used to establish the reference ranges of the ratio-based biomarkers by quantitative PCR or digital PCR. |
| |
| Bacterial infection samples | A retrospective sample of adult patients with positive bacterial blood culture. |
| |
| Tuberculosis samples | A retrospective sample of adult patients who were diagnosed to have active tuberculosis disease. |
|
| Name | Type | Description | Arm Group Labels | Other Names |
|---|---|---|---|---|
| No intervention | Other | No intervention for this retrospective study |
|
| Measure | Description | Time Frame |
|---|---|---|
| Viral host response Direct LS-TA in monocytes (Type I interferon response) | 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. | 1 day (first collected sample after admission) |
| Viral host response Direct LS-TA in granulocytes (Type I interferon response) | 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. | 1 day (first collected sample after admission) |
| Bacterial infection host response Direct LS-TA in monocytes (pro-inflammatory response) | 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. | 1 day (first collected sample after admission) |
| Bacterial infection host response Direct LS-TA in granulocytes (pro-inflammatory response) |
| Measure | Description | Time Frame |
|---|---|---|
| Reference intervals and median of these DIRECT LS-TA RBB in the control group | The median value and the central 95% range of each RBB will be determined. | 1 day (first collected sample after admission) |
Not provided
Inclusion Criteria:
Exclusion Criteria:
Not provided
Not provided
Not provided
Patients with Infections were patients admitted to ward for treatment of infection.
Not provided
Not provided
| Facility | Status | City | State | ZIP | Country | Contacts |
|---|---|---|---|---|---|---|
| Dept of Chemical Pathology, Chinese University of Hong Kong | Hong Kong | Hong Kong |
| PubMed Identifier | Type | Citation | Retractions |
|---|---|---|---|
| 40581066 | Background | Tang NLS, Kwan TK, Huang D, Ma SL, Leung KS. Direct single cell-type gene expression analysis in peripheral blood: novel ratio-based gene expression biomarkers using 2 novel monocyte reference genes (PSAP and CTSS) for detection of bacterial infection. Hum Mol Genet. 2025 Aug 21;34(17):1458-1470. doi: 10.1093/hmg/ddaf103. | |
| 34202032 |
| Label | URL |
|---|---|
| Patent about the model to obtain single cell-type gene expression in peripheral blood | View source |
Not provided
Descriptive statistics of each RBB (DIRECT LS-TA) will be provided on a reasonable request.
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Not provided
Blood are collected into EDTA or citrate tubes. An aliquot of whole blood (WB) will be processed for RNA fixation by addition of Trizol solution and stored in -70C before total RNA extraction. Another aliquot of WB are separated into granulocytes and PBMC by the Ficoll gradient method. Granulocytes and a portion of PBMC will be fixed by trizol.
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. |
| 1 day (first collected sample after admission) |
| Active TB host response Direct LS-TA in monocytes (Type II interferon response) | 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. | 1 day (first collected sample after admission) |
| Active TB host response Direct LS-TA in granulocytes (Type II interferon response) | 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. | 1 day (first collected sample after admission) |
| Huang D, Liu AYN, Leung KS, Tang NLS. Direct Measurement of B Lymphocyte Gene Expression Biomarkers in Peripheral Blood Transcriptomics Enables Early Prediction of Vaccine Seroconversion. Genes (Basel). 2021 Jun 25;12(7):971. doi: 10.3390/genes12070971. |
| 38268924 | Background | Huang B, Huang J, Chiang NH, Chen Z, Lui G, Ling L, Kwan MYW, Wong JSC, Mak PQ, Ling JWH, Lam ICS, Ng RWY, Wang X, Gao R, Hui DS, Ma SL, Chan PKS, Tang NLS. Interferon response and profiling of interferon response genes in peripheral blood of vaccine-naive COVID-19 patients. Front Immunol. 2024 Jan 10;14:1315602. doi: 10.3389/fimmu.2023.1315602. eCollection 2023. |
| Patent about the model to obtain single cell-type gene expression in peripheral blood | View source |
| ID | Term |
|---|---|
| D007239 | Infections |
| D014777 | Virus Diseases |
| D001424 | Bacterial Infections |
| D055985 | Latent Tuberculosis |
| D005334 | Fever |
| ID | Term |
|---|---|
| D001423 | Bacterial Infections and Mycoses |
| D014376 | Tuberculosis |
| D009164 | Mycobacterium Infections |
| D000193 | Actinomycetales Infections |
| D016908 | Gram-Positive Bacterial Infections |
| D000085343 | Latent Infection |
| D001832 | Body Temperature Changes |
| D012816 | Signs and Symptoms |
| D013568 | Pathological Conditions, Signs and Symptoms |
Not provided
Not provided