Clinical trial NCT06846645: Host Response to Infection by Direct Analysis of Leukocyte Single Cell-type Gene Expression/transcript Abundance, Direct LS-TA. a Prospective Study Will Evaluate the Performance of Direct LS-TA in Triage Febrile Patients Into Major Categories of Infections: Viral, Bacterial or Active Tuberculosis.
Official title: Peripheral Blood Single Cell-type Expression Profile of Interferon-stimulated and Other Biomarker Genes for Triage of Febrile Patients
Study type: OBSERVATIONAL
Overall status: NOT_YET_RECRUITING
Conditions: Single Cell Sequencing Technology
Gene Expression Profiling
Gene Expression
Infection
Viral Diseases
Bacterial Diseases
Active Tuberculosis
Host Defense Mechanisms
Host Microbial Interactions
Transcriptome
Keywords: host response
transcriptome
single cell-type gene expression
single cell RNA
triage
fever
febrile patient
Direct LS-TA
Lead sponsor: Chinese University of Hong Kong
Sponsor class: OTHER
First posted: 2025-02-26
Enrollment: 200
Sex: ALL
Minimum age (years): 18
Maximum age (years): 80
Standard ages: ADULT
OLDER_ADULT
Accepts healthy volunteers: no
Observational model: CASE_ONLY
Time perspective: PROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Patients with fever due to infections which are later clinically diagnosed as viral infection, bacterial infection or active tuberculosis.

Brief summary: Febrile illness is a common condition and it is crucial to have an early triage of patients according to various aetiologies to enable appropriate treatment. Currently, most screening/diagnostic tests target the detection of pathogens, while only a few assays aim to understand the host response, and they are mostly based on a measurement of serum proteins (e.g. CRP or procalcitonin).

Recently, blood transcriptome has been explored to differentiate bacterial and viral infections. However, gene expression in blood represents a composite score of gene expression of all the component cell-types present in the sample. Here, we propose to develop a rapid test that can determine gene expressions of a specified single cell type in peripheral blood (e.g., monocytes or granulocytes) as a host response biomarker 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 among various other leukocyte populations directly in a peripheral blood sample. Such results signify the nature of host response according to 3 or more axes (Type I or Type II interferon signaling response or pro-inflammatory cytokine signaling) And it can be used to indicate the type of underlying 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 the prospective study to evaluate and compare their diagnostic (triage) performance of febrile patients into different pathogen etiologies.

Comparing to other methods to obtain single cell-type gene expression data, DIRECT LS-TA has many advantages The conventional (gold standard) approach is to quantify gene expression in a sample of purified single cell-type from peripheral blood but it is very labour intensive procedure. Recent single-cell RNA sequencing can also provide gene expression data for every individual cell in a sample, but it is slow and very costly. DIRECT LS-TA provides the unique technique to quantify single cell-type gene expression in blood samples without the need to isolate the targeted cell-type. It has been used to differentiate the type of host response in fever patients into 3 major axes (Type I or Type II interferon signaling response or pro-inflammatory cytokine signaling) which correspond to the nature of underlying infection aetiologies (viral infection, active tuberculosis and bacterial infection).

See preprint DOI: 10.1101/2025.01.27.634977. and patents in B cells : https://patents.google.com/patent/WO2022089426A1/ Monocytes: https://patents.google.com/patent/WO2023109365A1/ Granulocytes : https://patents.google.com/patent/GB202400180D0/

Eligibility criteria: Inclusion Criteria:

* Adult patients with fever of acute onset which is defined by a raised body temperature.
* Patient should understand Chinese word to give informed consent.

Exclusion Criteria:

* Patients with a history of any immunodeficiency or immunocompromised condition. Patients received steriod or other immunotherapy.

Primary outcomes:
measure: Viral host response Direct LS-TA in monocytes (Type I interferon response)
timeFrame: first collected sample within the first week after admission
measure: Viral host response Direct LS-TA in granulocytes (Type I interferon response)
timeFrame: first collected sample within the first week after admission
measure: Bacterial infection host response Direct LS-TA in monocytes (pro-inflammatory response)
timeFrame: first collected sample within the first week after admission
measure: Bacterial infection host response Direct LS-TA in granulocytes (pro-inflammatory response)
timeFrame: first collected sample within the first week after admission
measure: Active TB host response Direct LS-TA in monocytes (Type II interferon response)
timeFrame: first collected sample within the first week after admission
measure: Active TB host response Direct LS-TA in granulocytes (Type II interferon response)
timeFrame: first collected sample within the first week after admission
Secondary outcomes:
measure: DIRECT LS-TA results distribution and median of these DIRECT LS-TA RBB in infection groups
timeFrame: first collected sample within the first week after admission
measure: Method evaluation to compare the performance of quantitative PCR and digital PCR
timeFrame: first collected sample within the first week after admission
Other outcomes:
Locations:
city: Hong Kong
country: Hong Kong
facility: Dept of Chemical Pathology, Chinese University of Hong Kong
Study officials:
References:
citation: 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.
citation: 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.