Shemesh, A. | Search bioRxiv

bioRxiv2021

Natural Killer cell division regulates FcεRIγ expression downstream of mTOR activity

The expansion of human Fc{varepsilon}RI{gamma}-/low (FcR{gamma}-/low) natural killer (NK) cells accrues during viral infections; however, the molecular mechanisms regulating FcR{gamma} expression is not well defined and can have implication for host protection and NK cell immunotherapy. Our analysis of NK cell subsets in lung transplant patients during rapamycin treatment revealed significantly lower FcR{gamma} levels in the NK cell population. Moreover, lower FcR{gamma} levels in healthy donors were associated with low mTORC1/C2 activity and low T-bet expression. Cell division suppression by rapamycin or TGF{beta} suppressed FcR{gamma} upregulation during IL-2 receptor stimulation, whereas promoting NK cell division by co-inhibiting FOXO1 activity restored FcR{gamma} upregulation. These results suggest that the human FcR{gamma}-/low NK cell phenotype is associated with cell division suppression and reduced mTOR activity.

immunology↗

bioRxiv2020

Combined protein and transcript single cell RNA sequencing reveals cardiovascular disease and HIV signatures

Cryopreserved peripheral blood mononuclear cells (PBMCs) are frequently collected and provide disease- and treatment-relevant data in clinical studies. Here, we developed combined protein (40 antibodies) and transcript single cell (sc)RNA sequencing in PBMCs. Among 31 participants in the WIHS Study, we sequenced 41,611 cells. Using Boolean gating followed by Seurat UMAPs and Louvain clustering, we identified 58 subsets among CD4 T, CD8 T, B, NK cells and monocytes. This resolution was superior to flow cytometry, mass cytometry or scRNA-sequencing without antibodies. Since the transcriptome was not needed for cell identification, combined protein and transcript scRNA-Seq allowed for the assessment of disease-related changes in transcriptomes and cell type proportion. As a proof-of-concept, we showed such differences between healthy and matched individuals living with HIV with and without cardiovascular disease. In conclusion, combined protein and transcript scRNA sequencing is a suitable and powerful method for clinical investigations using PBMCs.

immunology↗