Single-cell transcriptomics of blood reveals a natural killer cell subset depletion in tuberculosis

Abstract

Background: Tuberculosis (TB) continues to be a critical global health problem, which killed millions of lives each year. Certain circulating cell subsets are thought to differentially modulate the host immune response towards Mycobacterium tuberculosis (Mtb) infection, but the nature and function of these subsets is unclear. Methods: Peripheral blood mononuclear cells (PBMC) were isolated from healthy controls (HC), latent tuberculosis infection (LTBI) and active tuberculosis (TB) and then subjected to single-cell RNA sequencing (scRNA-seq) using 10 £ Genomics platform. Unsupervised clustering of the cells based on the gene expression profiles using the Seurat package and passed to tSNE for clustering visualization. Flow cytometry was used to validate the subsets identified by scRNA-Seq. Findings: Cluster analysis based on differential gene expression revealed both known and novel markers for all main PBMC cell types and delineated 29 cell subsets. By comparing the scRNA-seq datasets from HC, LTBI and TB, we found that infection changes the frequency of immune-cell subsets in TB. Specifically, we observed gradual depletion of a natural killer (NK) cell subset (CD3-CD7+GZMB+) from HC, to LTBI and TB. We further verified that the depletion of CD3-CD7+GZMB+ subset in TB and found an increase in this subset frequency after anti-TB treatment. Finally, we confirmed that changes in this subset frequency can distinguish patients with TB from LTBI and HC. Interpretation: We propose that the frequency of CD3-CD7+GZMB+ in peripheral blood could be used as a novel biomarker for distinguishing TB from LTBI and HC.

The inflammasome of circulatory collapse: single cell analysis of survival on extracorporeal life support

“…Conventional enumeration of peripheral blood mononuclear cells (PBMCs) and their subsets have failed to identify determinants of outcome among these cells for this complex patient population. Single cell transcriptomic approaches continue to modify and expand our understanding of the function and classification of PBMC subsets (2,3). The degree to which these sophisticated approaches will lead to clinically actionable information remains to be established (4).…”

Enabling out-of-clinic human immunity studies via single-cell profiling of capillary blood

“…Introduction: The advent of single-cell RNA sequencing (scRNA-seq) has enabled the interrogation of heterogeneous cell populations in blood without cell type isolation and has already been employed in the study of myriad immune-related diseases. 14,15,18 Recent studies employing scRNA-seq to study the role of immune cell subpopulations between healthy and ill patients, such as those for Crohn's disease 41 , Tuberculosis 40 , and COVID-19 39 , have identified cell typespecific disease relevant signatures in peripheral blood immune cells; however, these types of studies have been limited to large volume venous blood draws which can tax already ill patients, reduce the scope of studies to populations amenable to blood draws, and often require larger research teams to handle the patient logistics and sample processing costs and labor. In particular, getting repeated venous blood draws within a single day and/or multiple days at the subject's home has been a challenge for older people with frail skin and those on low dosage Acetylsalicylic acid.…”

The Role of Single-Cell Technology in the Study and Control of Infectious Diseases

“…In another study, PBMCs from patients with latent tuberculosis infection (LTBI) or active tuberculosis (TB), and from healthy individuals were analyzed with scRNA-seq [34]. T cells, B cells, and myeloid cells were distinguished, and 29 subsets were clustered.…”