Periodic Reporting for period 1 - ILCSIGNALLING (Deciphering cell-cell and cell-microbiome interactions of innate lymphoid cells at the single cell level)
Okres sprawozdawczy: 2018-01-01 do 2019-12-31
The key objective of this project is to develop a quantitative single-cell transcriptomics-based analysis method to gain comprehensive describe cells of the gastrointestinal system in health and disease, understanding of cell-to-cell communication network in the immune system in health and disease and decipher the impact of the microbiota. This is important, as dysregulation of the immune system of the gut leads to inflammatory diseases such as IBD, more severe outcomes of gastrointestinal infections and more severe outcomes of liver diseases. The objective of this study is to understand cellular and molecular mechanisms driving interactions between cells under stress in the disease model. We identified population of ILCs that are microbiota dependent, in absence of microbiota the number of ILC1 dramatically decreases, and these cells are replaced by ILC3p subpopulation. This leads to skewing the signalling balance in the liver, as ILC1 are producers of key soluble factors such as interferon gamma nad Ccl5. We also deeply characterised the process and found molecular mechanisms driving infiltration of monocytes to the liver upon liver damage. We observed amelioration of the acute liver failure in mouse model targeting TLR signalling, MAPK pathway, Myc transcription factor and microbiota, suggesting that these targets we have identified may indeed be clinically relevant. Hence, we demonstrated that a detailed ALF cellular decoding may enable pathway-specific therapeutic intervention.
Furthermore, I used the acetaminophen and thioacetamide ALF models to characterise over 40.000 single cell transcriptomes and to define the ALF cellular atlas. Using hierarchical clustering I identified 49 distinct populations and described their molecular states. Then I performed analysis of secretome and cell-to-cell interactions. The analysis of activation patterns revealed a common signature of 82-genes and further examination of promoters of these showed that MYC is a transcriptional regulator of this signature. MYC is driving expression of Ccl2 in stellate, Kupffer and endothelial cells which in turn drives infiltration of monocytes. Then we validated this using MYC inhibitors and flow cytometry, activity of liver enzymes in serum, histology and single cell sequencing. Then we performed experiments in germ free and antibiotics treated mice to examine the role of microbiota on the transcriptomic responses using single cell RNA sequencing and we were able to show that in absence of microbiota the responses are ameliorated and additionally there was less infiltration of monocytes. I validated this with flow cytometry, activity of liver enzymes in serum and histology. We hypothesised that microbiota as well as damage signal through the same pathway, i.e. TLR signalling and we used MyD88 Trif double knock out mice which do not have TLR signalling, because MyD88 and Trif are adaptor proteins of TLRs. With single cell RNA sequencing we found that in disease MyD88 Trif double knock out mice phenocopy MYC inhibition, suggesting that indeed TLR signalling is upstream MYC. We also tested inhibitors of MAPK pathway proteins (IRAK4, p38, TAK1, TPL2, RIP1 and ERK) in mouse disease models to find out which of the proteins mediate the signalling cascade and used flow cytometry to measure the extent of monocyte infiltration and liver damage with activity of liver enzymes in serum and histology.