Gene ExpressionNCT06838780
Host Response to Infection by Direct Analysis of Leukocyte Single Cell-type Gene Expression/transcript Abundance, Direct LS-TA
An observational study of Gene Expression and Gene Expression Profiling, run by Chinese University of Hong Kong at 1 site in Hong Kong.
Trial 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. Read more about this study
- Who is it for?
- Ages 18 years and olderHealthy volunteers can take part
- Conditions the study is for
- Gene Expression, Gene Expression Profiling, Infection
- How many people
- 192 participants
- Where
- 1 siteHong Kong
- Study dates
- 1 Jan 2018to 1 Jan 2026
- Phase
- Observational
- Are there results?
- Not yet: the study is under way
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages 18 years and older
- All sexes
- Healthy volunteers accepted
- Adult, Older adult
Study population: Patients with Infections were patients admitted to ward for treatment of infection.
Who may be able to join
- Bacterial infection sample: positive isolation of organism in blood culture (Bacterial infection sample group)
- Clinical diagnosed active TB (Tuberculosis infection group)
Who cannot join
- 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)
Trial locations and contacts
1 site in 1 country.
Hong Kong1 site
Dept of Chemical Pathology, Chinese University of Hong Kong
Hong Kong
About this study
Official title: Peripheral Blood Single Cell-type Expression Profile of Interferon-stimulated and Other Biomarker Genes for Triage of Febrile Patients
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).
Read the 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.
- Conditions
- Gene Expression, Gene Expression Profiling, Infection, Viral Diseases, Bacterial Infections, Active Tuberculosis
- Being tested
- No intervention
- Keywords
- host response, transcriptome, Single cell-type gene expression, triage, fever, febrile patients
- Medical subject headings
- Infections, Virus Diseases, Bacterial Infections, Latent Tuberculosis, Fever
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
No interventionOther
No intervention for this retrospective study
| Study group | Role | What they receive |
|---|---|---|
| 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. Receives: Other: No intervention | |
| Bacterial infection samples | A retrospective sample of adult patients with positive bacterial blood culture. Receives: Other: No intervention | |
| Tuberculosis samples | A retrospective sample of adult patients who were diagnosed to have active tuberculosis disease. Receives: Other: No intervention |
What is being measured
The primary outcome is the main question the study is designed to answer.
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.
Measured: 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.
Measured: 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.
Measured: 1 day (first collected sample after admission)
Bacterial infection host response Direct LS-TA in granulocytes (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: 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.
Measured: 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.
Measured: 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.
Measured: 1 day (first collected sample after admission)
Secondary outcomes (1)
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.
Measured: 1 day (first collected sample after admission)
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted21 Feb 2025
- Study start1 Jan 2018
- Primary completion1 Jan 2026 (estimated)
- Study completion1 Jan 2026 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Publications (3)Papers the sponsor has linked to this study.
- Other trials for Gene ExpressionStudies of the same condition, open and under way.
- More trials run by Chinese University of Hong KongThe sponsor's other registered studies.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Observational
- Observational model
- Case-control
- Time perspective
- Retrospective
- Enrolment
- 192 participants (actual)
Sponsor and investigators
- Lead sponsor
- Chinese University of Hong Kong
- Sponsor type
- University, hospital or other
- Responsible party
- Principal investigator, Nelson Tang, Chinese University of Hong Kong
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT06838780
- Sponsor's protocol ID
- Direct LS-TA retrospective
- Status last verified
- Feb 2025
- First submitted
- 17 Feb 2025
- Last updated
- 3 Mar 2025
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- Undecided: Descriptive statistics of each RBB (DIRECT LS-TA) will be provided on a reasonable request.
Publications
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.
PubMed 40581066Huang 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.
PubMed 34202032Huang 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.
PubMed 38268924
Study at a glance
From the registry record, last updated by the sponsor on 3 Mar 2025. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Peripheral Blood Single Cell-type Expression Profile of Interferon-stimulated and Other Biomarker Genes for Triage of Febrile Patients
- ClinicalTrials.gov ID
- NCT06838780
- Acronym / sponsor ID
- Direct LS-TA retrospective
- Conditions
- Gene Expression, Gene Expression Profiling, Infection, Viral Diseases, Bacterial Infections, Active Tuberculosis
- Keywords
- host response, transcriptome, Single cell-type gene expression, triage, fever, febrile patients
- Study type
- Observational
- Recruitment status
- Active, not recruiting
- Enrolment
- 192 participants (actual)
- Lead sponsor
- Chinese University of Hong KongUniversity, hospital or other
- Study start
- 1 Jan 2018 (actual)
- Primary completion
- 1 Jan 2026 (estimated)
- Study completion
- 1 Jan 2026 (estimated)
- First posted
- 21 Feb 2025 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
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.
Study design
- Observational model
- Case-control
- Time perspective
- Retrospective
- Number of arms
- 3
| Arm | Type | Receives |
|---|---|---|
| Vaccination Controls | – | Other: No interventionUp 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 | – | Other: No interventionA retrospective sample of adult patients with positive bacterial blood culture. |
| Tuberculosis samples | – | Other: No interventionA retrospective sample of adult patients who were diagnosed to have active tuberculosis disease. |
Who may qualify
- Ages
- 18 years and older
- Sex
- All
- Healthy volunteers
- Accepted
- Age groups
- Adult, Older adult
- Study population
- Patients with Infections were patients admitted to ward for treatment of infection.
Key inclusion criteria (2 listed)
- Bacterial infection sample: positive isolation of organism in blood culture (Bacterial infection sample group)
- Clinical diagnosed active TB (Tuberculosis infection group)
Key exclusion criteria (3 listed)
- 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)
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| No interventionNo intervention for this retrospective study | Other | Bacterial infection samples, Tuberculosis samples, Vaccination Controls |
Primary outcome
Viral host response Direct LS-TA in monocytes (Type I interferon response)
Time frame: 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)
Time frame: 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.
Bacterial infection host response Direct LS-TA in monocytes (pro-inflammatory response)
Time frame: 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.
Bacterial infection host response Direct LS-TA in granulocytes (pro-inflammatory response)
Time frame: 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)
Time frame: 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.
Active TB host response Direct LS-TA in granulocytes (Type II interferon response)
Time frame: 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.
1 secondary outcome
Reference intervals and median of these DIRECT LS-TA RBB in the control group
Time frame: 1 day (first collected sample after admission)
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 3 Mar 2025.
- Background: PubMed 40581066Tang 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.
- Background: PubMed 34202032Huang 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.
- Background: PubMed 38268924Huang 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 bloodLink provided by the sponsor.
- Patent about the model to obtain single cell-type gene expression in peripheral bloodLink provided by the sponsor.
- Individual participant dataSharing planned: Undecided. Descriptive statistics of each RBB (DIRECT LS-TA) will be provided on a reasonable request.
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Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part. This study is not recruiting at the moment.
The record lists no contact. Use the official record to reach the sponsor.
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
An observational study of Gene Expression and Gene Expression Profiling, run by Chinese University of Hong Kong at 1 site in Hong Kong.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 2 inclusion and 3 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: under way, not looking for participants, as of the sponsor's last update on 3 Mar 2025. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in Hong Kong. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Viral host response Direct LS-TA in monocytes (Type I interferon response) (time frame: 1 day (first collected sample after admission)). The study lists 6 primary outcomes in all. It is what the study was designed to measure, not a finding.
Where can I read the original study information?
On the ClinicalTrials.gov record for NCT06838780, which also lists 3 linked publications.
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 3 Mar 2025.