Elucidation of Natural Killer T cell development in a mice model of rheumatoid arthritis

2020 Fiscal Year Research-status Report

• Project/Area Number: 20K07538
• Research Institution: Osaka University
• Principal Investigator: ディエス ディエゴ 大阪大学, 免疫学フロンティア研究センター, 准教授 (90597741)
• Project Period (FY): 2020-04-01 – 2023-03-31
• Keywords: Immunology / Bioinformatics / Systems immunology

Outline of Annual Research Achievements

1. We have performed single cell transcriptomics coupled with protein expression and immune repertoire of NKT cells from the thymus and spleen of WT and SKG mice. NKT cells were sorted as CD3+CD1D-tet+CD19- cells. The samples were processed with 10x chromium platform and the resulting sequencing products processed with the cellranger software.
2. Analysis of the TCR repertoire confirmed that the majority of assayed cells were consistent with expression of TCR with invariant alpha chain.
3. We analyzed the single cell data in R, calculated PCA and UMAP plots and performed clustering. We performed differential gene expression and identified several populations of NKT cells: proliferative, cycling, apoptotic and NKT1, NKT2 and NKT17 subtypes.
4. As reported previously NKT1 cells were more abundant in SKG mice, whereas NKT2 were more abundant in WT (Balb/c) mice. We found that proliferative cells were more abundant in SKG mice.6. NKT cells in SKG mice have higher expression of PLZF transcription factor. This protein regulates the expression of the transcriptional program promoting NKT1 subtype.
5. We performed transcriptional regulatory network analysis and identified clusters of regulators associated with each cell subtypes.

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

We have performed the planned single cell genomics experiments as scheduled.

Strategy for Future Research Activity

We have extended the original plan with an additional experiment looking at transcriptome and chromatin accessibility (ATAC) at the single cell level. The results from that additional experiment will be obtained in the coming months. We will perform combined analysis of the original dataset (single cell transcriptome, protein expression and immune repertoire) with the experiment currently underway (single cell transcriptome and chromatin accessibility). This will enable us to uncover the changes in transcriptional regulatory networks associated with the development of NKT cells, and what transcription factors and target genes are affected in SKG mice.

Causes of Carryover

We will finish the experiments and start writing the manuscript. We expect to be able to send the paper for publication and present the results in international conference this year.