Single-cell analysis of intestinal lymphocytes reveals targets for treatment of inflammatory bowel disease

Project Information

GUT-SEQ

Grant agreement ID: 850963

DOI

10.3030/850963

EC signature date 30 January 2020

Start date 1 September 2020

End date 31 August 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 500 000,00

EU contribution

€ 1 500 000,00

Coordinated by

KAROLINSKA INSTITUTET
Sweden

Periodic Reporting for period 3 - GUT-SEQ (Single-cell analysis of intestinal lymphocytes reveals targets for treatment of inflammatory bowel disease)

Reporting period: 2023-09-01 to 2025-02-28

Summary of the context and overall objectives of the project

Inflammatory bowel disease (IBD) constitutes an increasing global health burden and improved treatment of this disease would reduce individual suffering but also societal costs. Current biological IBD treatments that specifically target the immune system are not effective in all patients with IBD. Hence, there is an urgent need to identify the patients that will respond to current drugs, as well as to identify additional treatment targets in IBD. To achieve this, a better understanding of the human intestinal immune system is needed. My group has made seminal contributions to the discovery and characterization of a novel family of immune cells in humans, so called innate lymphoid cells (ILCs). Our work has revealed that in addition to T cells, which are known drivers of IBD, ILCs play important roles in the gut during both health and disease. However, the exact contributions of ILCs and T cells to IBD, and how these immune cells could be used to predict and characterize the response to IBD treatment, is unknown. Hence, the overall objective of this proposal is to perform a comprehensive characterization of the human intestinal ILCs and T cells in the healthy and inflamed intestine, including compartmentalization studies. Using this information, we will then address if subsets of ILCs and T cells could have a value in predicting and characterizing the response to novel biological treatments in IBD.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In aim 1 of the proposal we set out to perform a comprehensive molecular dissection to determine parallels between known, and identify novel, subsets of human intestinal tissue-resident, inflammation-associated, lymphocytes of IBD patients using transcriptional analysis on the single cell level (scRNA-seq) as well as epigenetic analysis (ATAC-seq). In this aim we have completed large parts of all three work packages (WP1-3). For WP1 we have performed a comparison between innate (ILCs) and adaptive lymphocytes (T cells) in colonic mucosa of patients with IBD to reveal shared but also unique transcriptional programs in these cells (Kokkinou et al, Cell Rep Med, accepted for publication). Parts of WP2 was published in 2021 (Mazzurana et al, Cell Res, 2021) where we performed a single-cell transcriptional characterization of ILCs in gut, lung, blood and tonsil of healthy donors. We are currently addressing the transcriptional characteristics of ILCs and T cells depending on localization in the healthy and inflamed gut (Stamper et al, work in progress). In WP3 we have performed a thorough characterization of the transcriptional (RNAseq), epigenetic (ATACseq), functional and metabolic characteristics of progenitors of ILCs in mucosal tissues including the inflamed IBD gut (Kokkinou et al, Science Immunology, 2022).

In aim 2 we are working to unveil critical disease mechanisms, immunological signatures of treatment response and drug-induced immunological changes through longitudinal assessments of human intestinal lymphocytes from IBD patients on novel biological treatments. In this aim we have collected longitudinal samples from 35 IBD patients that have started biologics treatment. Cells have been isolated and biobanked to be analysed once aim 1 is completed.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Aim 1 has progressed very well and we have already published three high impact papers that enhance the understanding of the human gut immune environment during health and disease. More specifically, we have described how ILCs are specifically imprinted by the gut microenvironment relative to other tissues such as the blood, lung and tonsils (Mazzurana et al, Cell Res, 2021). We have also shown that progenitors of ILCs are present in the gut mucosa and which factors that regulate their function (Kokkinou et al, Sci Imm, 2022). The transcriptional, epigenetic, functional and metabolic characteristics of such ILC progenitors was also described (Kokkinou et al, Sci Imm, 2022). We have also shown the relative role of ILCs and T cells in the gut mucosa in patients with IBD and how both innate and adaptive lymphocytes are altered during inflammation (Kokkinou et al, Cell Rep Med, accepted). In terms of localization of ILCs and T cells in the gut mucosa, we have so far generated data for half of the samples that we set out to analyze, and the project is progressing well.
At the end of aim 1 we expect to have a comprehensive understanding of the relative role of ILCs and T cells in different compartments of the human colon in health and IBD.
For aim 2, biobanking of longitudinal samples from patients treated with biologic therapy is ongoing and we aim to start analyzing the first group of samples at the end of 2023.
At the end of aim 2 we expect to have revealed an immunological signature of successful response to biologics therapy, and identified biomarkers that can aid in predicting which patients will respond to biologics.