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Published on: December 3, 2019
Multidimensional Clusters of CD4+ T Cell Dysfunction Are Primarily Associated with the CD4/CD8 Ratio in Chronic HIV
Juliet Frederiksen1, Marcus Buggert2, Kajsa Noyan3
1Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
Insights
This study identified specific CD4+ T cell clusters linked to HIV disease progression. The CD4/CD8 ratio effectively measures combined CD4+ T cell dysfunction in chronic HIV infection.
Area of Science:
- Immunology
- Virology
- Computational Biology
Background:
- HIV infection causes significant immune system damage, particularly affecting CD4+ T cells.
- Previous research often focused on limited markers of immune dysfunction, leaving pathological CD4+ T cell clusters understudied.
- Identifying specific CD4+ T cell clusters associated with HIV disease biomarkers is crucial for understanding disease progression.
Purpose of the Study:
- To investigate immune activation, exhaustion, and senescence in CD4+ T cells using multi-parametric flow cytometry.
- To compare manual data analysis with a multidimensional clustering tool (FLOCK) for identifying pathological CD4+ T cell clusters.
- To establish reliable biomarkers for HIV disease progression by correlating laboratory parameters with identified CD4+ T cell clusters.
Main Methods:
- Multi-parametric flow cytometry was employed to analyze CD4+ T cell phenotypes in HIV-infected individuals and healthy controls.
- A novel "artificial reference" method was developed to reduce subjectivity in FLOCK analysis.
- Principle component analysis and multiple correlation analyses were used to compare data analysis methods and identify disease biomarkers.
Main Results:
- The "artificial reference" method improved the separation of HIV-infected individuals from healthy controls compared to manual analysis or single-subject references.
- The CD4/CD8 ratio emerged as the most significant surrogate marker for CD4+ T cell dysfunction across all analysis methods.
- An early-differentiated CD4+ T cell cluster expressing CD38, HLA-DR, and PD-1 showed the strongest correlation with HIV disease progression, as indicated by the CD4/CD8 ratio.
Conclusions:
- The novel clustering approach effectively identifies cell clusters distinguishing healthy from HIV-infected subjects.
- The identified CD4+ T cell clusters are biologically relevant to HIV disease progression.
- The CD4/CD8 ratio serves as a valuable and simple biomarker for assessing combined CD4+ T cell dysfunction in chronic HIV disease.
Abstract:
HIV infection provokes a myriad of pathological effects on the immune system where many markers of CD4+ T cell dysfunction have been identified. However, most studies to date have focused on single/double measurements of immune dysfunction, while the identification of pathological CD4+ T cell clusters that is highly associated to a specific biomarker for HIV disease remain less studied. Here, multi-parametric flow cytometry was used to investigate immune activation, exhaustion, and senescence of diverse maturation phenotypes of CD4+ T cells. The traditional method of manual data analysis was compared to a multidimensional clustering tool, FLOw Clustering with K (FLOCK) in two cohorts of 47 untreated HIV-infected individuals and 21 age and sex matched healthy controls. In order to reduce the subjectivity of FLOCK, we developed an "artificial reference", using 2% of all CD4+ gated T cells from each of the HIV-infected individuals. Principle component analyses demonstrated that using an artificial reference lead to a better separation of the HIV-infected individuals from the healthy controls as compared to using a single HIV-infected subject as a reference or analyzing data manually. Multiple correlation analyses between laboratory parameters and pathological CD4+ clusters revealed that the CD4/CD8 ratio was the preeminent surrogate marker of CD4+ T cells dysfunction using all three methods. Increased frequencies of an early-differentiated CD4+ T cell cluster with high CD38, HLA-DR and PD-1 expression were best correlated (Rho = -0.80, P value = 1.96×10-11) with HIV disease progression as measured by the CD4/CD8 ratio. The novel approach described here can be used to identify cell clusters that distinguish healthy from HIV infected subjects and is biologically relevant for HIV disease progression. These results further emphasize that a simple measurement of the CD4/CD8 ratio is a useful biomarker for assessment of combined CD4+ T cell dysfunction in chronic HIV disease.
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