ECCO Pioneer Award Synopsis: Daniel Kotlarz

Daniel Kotlarz, ECCO Grant Awardee

Decoding molecular mechanisms and druggable targets of VEO-IBD by multimodal single-cell profiling

Daniel Kotlarz
© Daniel Kotlarz


The pathogenesis and course of Inflammatory Bowel Disease (IBD) are heterogeneous and have striking age-dependent characteristics. In particular, children with very early-onset IBD (VEO-IBD) show a higher incidence of unclassified IBD and develop courses different from adult-onset forms. VEO-IBD is a rare condition, but the incidence is increasing globally at an alarming pace. Notably, VEO-IBD patients often fail to respond to conventional therapies and show life-threatening conditions.

In paradigmatic studies, we have previously reported IL-10R deficiencies as a monogenic cause in children with intractable VEO-IBD. Based on knowledge of the molecular disease mechanisms, IL-10R-deficient patients could be cured by allogeneic haematopoietic stem cell transplantation. This prime example of translational research has shifted paradigms by demonstrating the relevance of genetics for the treatment of VEO-IBD patients. Our genetic screen of one of the largest international VEO-IBD cohorts has revealed disease-causing mutations in approximately 20% of analysed patients (>60 genetic entities) and suggested optimised treatment for a significant number of children. However, most VEO IBD patients still lack definitive diagnosis and the disease mechanisms remain largely elusive.

Our ECCO-funded project aims to uncover novel genetic signatures and disease mechanisms underlying VEO-IBD by complementing genome-wide sequencing with advanced single-cell RNA sequencing. We postulate that our systems biology approach will:

  • advance the knowledge on basic molecular principles of intestinal inflammation
  • increase the diagnostic yield of monogenic IBD
  • highlight polygenic risk factors of VEO-IBD
  • unravel druggable phenotypes of intestinal inflammation

Since VEO-IBD represents a “powerful disease model” to define key regulators of intestinal inflammation, our studies will also provide transformational insights into mechanisms and therapeutic targets for common IBD.


Intestinal inflammation is characterised by alterations in tissue composition and cell-intrinsic programs. In our ECCO-funded project, we propose complementing genome-wide sequencing by multimodal single-cell transcriptome profiling of intestinal biopsies from VEO-IBD patients. Innovative CITE-seq will combine single-cell gene expression profiling with antibody-based detection of >100 cellular surface proteins, providing a comprehensive understanding of cellular diversity and function in complex intestinal tissues (directly at the site of inflammation). Best practice computational workflows for single-cell data processing will be applied to characterise cell type-specific disease states by analysing cellular compositions, gene expression programs, cell fate trajectories and inferences of cell–cell interaction networks. The integration of genomic data and single-cell disease signatures will create a VEO-IBD atlas serving as a blueprint to improve diagnostic rates and discover personalised therapies for children with a devastating condition.

Proposed Timing

In the first year of the funding period, colonic biopsies from VEO-IBD patients will be collected for multimodal single-cell profiling. In the last quarter of the first year, we will initiate generation of scRNA-seq data and optimise our analysis pipeline to decipher cellular disease states of intestinal inflammation. In the second year, we will shift the focus to identifying novel genetic factors of IBD by linking disease signatures with potential causal variants. During the last six months, shared and distinct disease signatures between rare and common forms of IBD will be explored using publicly available single-cell data sets.

Posted in ECCO News, SciCom, Committee News, Volume 18, Issue 2, Fellowships & Grants Synopsis Reports