Periodic Reporting for period 3 - EnviroTag (Unbiased niche identification and manipulation in stem cells and cancer)
Reporting period: 2024-03-01 to 2025-08-31
Cellular micro-environments, often referred to as "niches," play a pivotal role in orchestrating the destiny of individual cells. During normal cell turnover in organs, these specialized niches steer cells towards distinct paths of specialization. This intricate guidance ensures the functional diversity within the organ's cellular composition. Other niches, particularly those surrounding adult tissue stem cells are indispensable for maintaining stemness and thus the regenerative capabilities of organs. Even after catastrophic stem cell loss, specialized micro-environments (e.g. in the intestine) possess the remarkable capacity to reprogram differentiated cells, reverting them to an adult stem cell state. Consequently, cellular identity within epithelial organs is intrinsically interwoven with its spatial context. This spatial context emerges as a critical determinant in upholding organ functionality and facilitating regenerative processes, yet it holds equal relevance for disease.
Notably, similar to adult tissue stem cells, cancer cells also rely on specific micro-environments for their survival and expansion. This dependence is particularly pronounced during the initial stages of metastasis, when cancer cells find themselves without an established supportive tumor microenvironment at the distant site. The nature and suitability of this niche determine the fate of these cancer cells: death, dormancy, or aggressive proliferation. Even if cancer cells do find a suitable microenvironment for initial survival, the tumor cells need to remodel the cellular composition around them to ensure sufficient supply of nutrients, escape from immune detection and stimulation of growth promoting signaling pathways. At the same time, the changing niche conditions change cancer cell behavior. Success or failure of this co-evolution of metastatic cells and niche cells ultimately determines disease outcome and thus ultimately affects patient survival.
Despite the pivotal role of these cellular niches in normal physiology and disease, our understanding of their composition and the dynamic alterations they undergo during tissue regeneration or metastatic expansion is still very limited. One of the main reasons for this lack of knowledge is that few suitable tools exist to study these local cell communities with single-cell resolution. The EnviroTag project aims to close this knowledge gap and establish a novel reporter system, capable of selectively studying small and rare microenvironments such as those of adult tissue stem cells and early metastatic cancer cells. Our research objectives, which focus primarily on the gastrointestinal system, encompass not only the generation of a deeper understanding of microenvironmental dynamics but also the identification of novel regulatory mechanisms, signaling pathways, and specific cell types that may serve as potential targets for enhancing tissue regeneration or impeding the spread of metastatic disease.
Notably, similar to adult tissue stem cells, cancer cells also rely on specific micro-environments for their survival and expansion. This dependence is particularly pronounced during the initial stages of metastasis, when cancer cells find themselves without an established supportive tumor microenvironment at the distant site. The nature and suitability of this niche determine the fate of these cancer cells: death, dormancy, or aggressive proliferation. Even if cancer cells do find a suitable microenvironment for initial survival, the tumor cells need to remodel the cellular composition around them to ensure sufficient supply of nutrients, escape from immune detection and stimulation of growth promoting signaling pathways. At the same time, the changing niche conditions change cancer cell behavior. Success or failure of this co-evolution of metastatic cells and niche cells ultimately determines disease outcome and thus ultimately affects patient survival.
Despite the pivotal role of these cellular niches in normal physiology and disease, our understanding of their composition and the dynamic alterations they undergo during tissue regeneration or metastatic expansion is still very limited. One of the main reasons for this lack of knowledge is that few suitable tools exist to study these local cell communities with single-cell resolution. The EnviroTag project aims to close this knowledge gap and establish a novel reporter system, capable of selectively studying small and rare microenvironments such as those of adult tissue stem cells and early metastatic cancer cells. Our research objectives, which focus primarily on the gastrointestinal system, encompass not only the generation of a deeper understanding of microenvironmental dynamics but also the identification of novel regulatory mechanisms, signaling pathways, and specific cell types that may serve as potential targets for enhancing tissue regeneration or impeding the spread of metastatic disease.
In the course of the EnviroTag project, we successfully developed two new spatial reporter systems that utilize complementary modes of action to identify either niche cells in direct contact or niche cells in paracrine range of a cell of interest. After in vitro validation, we have already moved one of the systems to the in vivo setting to study early metastatic niche composition and dynamics in colorectal cancer. The resulting imaging and single-cell sequencing dataset gives us unprecedented insight into metastatic niche evolution and enables us to identify critical cellular interactions that may be targeted to prevent metastatic progression. We selected multiple candidate interactions that we are now following-up on to determine their individual role in colorectal cancer metastasis.
Beyond our cancer-related work, we also made progress in building a generalized EnviroTag system that would enable niche identification of any cell of interest in vivo. To this end, we are currently generating multiple new mouse strains that incorporate EnviroTag technology. These animals will support our efforts to investigate dynamic changes in adult stem cell niche compositions during homeostasis and after injury.
Beyond our cancer-related work, we also made progress in building a generalized EnviroTag system that would enable niche identification of any cell of interest in vivo. To this end, we are currently generating multiple new mouse strains that incorporate EnviroTag technology. These animals will support our efforts to investigate dynamic changes in adult stem cell niche compositions during homeostasis and after injury.
To date the EnviroTag project has reached two main goals that enable a significant advance in our understanding of the dynamic interactions between healthy and malignant epithelial cells with their respective niche. On the one hand, the development of two highly sensitive EnviroTag reporter systems with spatial resolution enables the precise identification and isolation of niches around rare cell populations and individual cells, filling a critical gap in spatial biology research. On the other hand, the generation of a comprehensive single-cell atlas of colorectal cancer metastasis, featuring both spatial and temporal resolution, represents an important step in understanding and the complex process of metastatic growth. This atlas will not only serve as a valuable resource for the scientific community but also facilitate the modeling of interactions between different cell populations within the metastatic niche.
In the second half of the project, we will leverage this powerful tool and explore the role of candidate interactions in the niche environment. Thereby, we aim to identify critical mechanisms of cancer cell – niche interactions that can be disrupted to prevent metastatic seeding at distant sites. To do so, we will employ in vitro experiments in organoids combined with in vivo validation in the mouse.
In parallel, we will further expand the EnviroTag toolbox and generate a complementary niche dataset on homeostatic and injured adult stem cell niches along the gastrointestinal tract. This dataset will enable us to understand the necessary changes that stem cell niches undergo to activate regenerative responses and will highlight the common and distinctive features of healthy stem cell environments and metastatic niches. Ultimately, this dataset will enable us to identify mechanisms of adult stem cell control and induced plasticity that may eventually be employed to restore lost regenerative capacity in gastrointestinal organs.
In the second half of the project, we will leverage this powerful tool and explore the role of candidate interactions in the niche environment. Thereby, we aim to identify critical mechanisms of cancer cell – niche interactions that can be disrupted to prevent metastatic seeding at distant sites. To do so, we will employ in vitro experiments in organoids combined with in vivo validation in the mouse.
In parallel, we will further expand the EnviroTag toolbox and generate a complementary niche dataset on homeostatic and injured adult stem cell niches along the gastrointestinal tract. This dataset will enable us to understand the necessary changes that stem cell niches undergo to activate regenerative responses and will highlight the common and distinctive features of healthy stem cell environments and metastatic niches. Ultimately, this dataset will enable us to identify mechanisms of adult stem cell control and induced plasticity that may eventually be employed to restore lost regenerative capacity in gastrointestinal organs.