Single-cell RNA-seq reveals alterations in peripheralCX3CR1and nonclassical monocytes in familial tauopathy

Abstract

Background: Emerging evidence from mouse models is beginning to elucidate the brain's immune response to tau pathology, but little is known about the nature of this response in humans. In addition, it remains unclear to what extent tau pathology and the local inflammatory response within the brain influence the broader immune system. Methods: To address these questions, we performed single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from carriers of pathogenic variants in MAPT, the gene encoding tau. Results: Analysis of ~181,000 individual PBMC transcriptomes from MAPT pathogenic variant carriers (n = 8) and healthy non-carrier controls (n = 8) demonstrated striking differential expression in monocytes and natural killer (NK) cells. We observed a marked reduction in the expression of CX3CR1 - the gene encoding the fractalkine receptor that is known to modulate tau pathology in mouse models - in monocytes and NK cells. We also observed a significant reduction in the abundance of nonclassical monocytes and dysregulated expression of nonclassical monocyte marker genes, including FCGR3A. Finally, we identified reductions in TMEM176A and TMEM176B, genes thought to be involved in the inflammatory response in human microglia. We confirmed differential expression of select biologically relevant genes dysregulated in our scRNA-seq data using droplet digital PCR as an orthogonal technique for quantitative validation. Conclusions: Our results suggest that human peripheral immune cell expression and abundance are modulated by tau-associated pathophysiologic changes. CX3CR1 and nonclassical monocytes in particular will be a focus of future work exploring the role of these peripheral signals in additional tau-associated neurodegenerative diseases.

Expansion of highly interferon-responsive T cells in early-onset Alzheimer’s disease

“…We found that the expansion of ISAG hi T cells relative to PBMCs and all T cells remained significant after addition of these independent controls, although one outlier control sample with very high levels of ISAG hi T cells made the findings somewhat less robust (eFigure 2). We recently reported a reduction in peripheral non-classical monocytes in familial tauopathy 5 . Comparing the familial tauopathy and EOAD datasets, we found that non-classical monocytes are not reduced in EOAD, and ISAG hi T cells are not expanded in familial tauopathy (eFigure 3).…”

“…After obtaining informed consent, PBMCs from study participants (Table 1) at the University of California, San Francisco Memory and Aging Center were analyzed by scRNA-seq essentially as described 5 . Details are described in eMethods.…”

“…After obtaining informed consent, PBMCs from study participants (Table 1) at the University of California, San Francisco Memory and Aging Center (MAC) were analyzed by scRNA-seq essentially as described [5]. Raw sequencing reads were aligned to GRCh38-2020-A and feature-barcode matrices generated using Cell Ranger (v7.1.0) with intronic reads excluded.…”

Expansion of highly interferon‐responsive T cells in early‐onset Alzheimer's disease

“…To increase the sample size of our scRNA-seq dataset, we included seven additional control PBMC samples previously characterized by scRNA-seq. 5 We found that the expansion of ISAG hi T cells relative to PBMCs and all T cells remained significant after addition of these independent controls, despite a single outlier control sample with very high levels of ISAG hi T cells (Supplementary Figure S2). We recently reported a reduction in peripheral non-classical monocytes in familial tauopathy.…”

“…After obtaining informed consent, PBMCs from study participants (Table 1) at the University of California, San Francisco Memory and Aging Center (MAC) were analyzed by scRNA-seq essentially as described. 5 Raw sequencing reads were aligned to GRCh38-2020-A and feature-barcode matrices were generated using Cell Ranger Additional details, including bioinformatic and experimental methods, are described in the Supplementary Methods document and Supplementary Tables S1-S3.…”