Open Research Projects, Research

Establishment of human colon assembloids to study the regulatory networks between epithelial crypts and the surrounding niche

Prinicipal Investigator

Prof. Dr. Michael Sigal
Dr. Manqiang Lin

Scientific interest within the context of the graduate college:

The gastrointestinal epithelium is organized into clonal crypts that represent sophisticated anatomical and functional tissue units. The epithelium is intimately associated with the mesenchymal stroma network, and various mesenchymal cell types are essential constituents of the stem cell niche that regulates epithelial homeostasis. The gastrointestinal stem cells give rise to differentiated cells. This process is important to maintain the nutritive absorptive functions of the epithelium as well as to build a barrier against pathogens and toxins from the environment. Recently, it has become increasingly evident that interactions between the epithelium and stroma are vital in regulating the barrier function, allowing tissue adaptations to environmental perturbations1,2. Our research aims at understanding the interplay between the epithelium, stroma and the microbiota. We would like to understand how tissues respond to microbiota alterations or exposure to pathogenic bacteria as well as their toxins. To address this, we are also developing new organoid and assembloid models to recapitulate the cellular networks observed in vivo.

Project description:

Introduction: The cellular organization of gastrointestinal crypts is regulated by various cells in the surrounding mesenchymal niche, which guide stem cell self-renewal and turnover. Environmental factors such as bacterial virulence, chemicals, and radiation can alter the mesenchymal niche. The interaction between the epithelium and its microenvironment allows the mucosal barrier to react quickly to harmful factors and maintain homeostasis. Exploring how the epithelial and mesenchymal compartments communicate and self-organize could provide new insights into disease prevention and therapy development.

Currently, 3D gastrointestinal organoids are the standard for studying epithelial cell behavior, but the absence of mesenchymal cells in this system limits the analysis of the interplay between the epithelium and connective tissue4. Therefore, we aim to establish a novel co-culture system, called assembloids, by combining human colonic epithelial and mesenchymal cells in a single structure, to dissect epithelial-mesenchymal interactions in a tractable manner. Using the assembloid system, we can investigate whether stromal cells promote the formation of true colonic crypts that resemble the in vivo anatomy and cellular organization. Next, we plan to establish a vessel network and incorporate immune cells in assembloids to mimic a functional mucosal barrier. We will also study whether the assembloid model can resemble the mucosal response to environmental factors, helping us understand how health is maintained in the human gastrointestinal tract.

Aim 1: Generate human colon assembloids, characterize the various stromal cells, investigate how the stromal compartment in assembloids guides epithelial crypt maturation.

Aim 2: Optimize the culture conditions required for the formation of vessel networks and incorporation of macrophages in assembloids. Explore the interplay between macrophages and stromal cells.

Aim 3: Expose assembloids to bacteria and their virulence factors, to explore mechanisms that guide the response of mucosa to environmental factors.

Application details


  1. Sigal M, Logan CY, Kapalcynska M, […], Nusse R, Amieva MR, Meyer TF. Stromal R-spondin orchestrates gastric epithelial stem cells and gland homeostasis. Nature. 2017; 548:451-455. doi: 10.1038/nature23642.
  2. Kapalczynska M, Lin M, Maertzdorf J, […], Tacke F, Meyer TF, Sigal M. BMP feed-forward loop promotes terminal differentiation in gastric glands and is interrupted by H. pylori-driven inflammation. Nat Commun. 2022; 13:1577. doi: 10.1038/s41467-022-29176-w.
  3. Heuberger J, Trimpert J, Vladimirova D, […], Tacke F, Osterrieder N, Sigal M. Epithelial response to IFN-gamma promotes SARS-CoV-2 infection. EMBO Mol Med. 2021; 13:e13191. doi: 10.15252/emmm.202013191.
  4. Sato T, Vries RG, Snippert HJ, […], Kujala P, Peters PJ, Clevers H. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature. 2009; 459:262-265. doi: 10.1038/nature07935.