Organ Homeostasis & Physiology Lab

Novo Nordisk Foundation Young Investigator Award 2020-2026

Horizon Europe MSCA European Postdoctoral Fellowship- Alphy John 2024-2026

ERC Starting Grant 2019-2024

Novo Nordisk Foundation Project Grants in Bioscience and Basic Biomedicine 2021-2023

Adult tissues with high turnover rates, such the intestine, depend on stem cells (SCs) to provide a continuous source of differentiated cells to maintain tissue homeostasis. To ensure optimal tissue homeostasis and physiology, adult stem cells must coordinate their own maintenance with the generation of differentiated cell types in a temporally and spatially controlled manner. Due to its remarkable self-renewing capacity, the fly gut has recently become a prime paradigm for studying stem-cell function during adult tissue homeostasis. This capacity for self-renewal relays on the proliferative activity of the intestinal stem cells (ISC), which is tightly coupled with cell loss to maintain intestinal homeostasis. ISC proliferation is controlled by multiple local and systemic signals released from the ISC niche (enterocytes (ECs), enteroendocrine cells (EECs), enteroblasts (EBs), and visceral muscles (VMs)) and non-gastrointestinal organs. Deregulation of ISC proliferation affects gut integrity, which in turn can trigger several chronic inflammatory diseases including colorectal cancer. Identifying niche-derived and systemic signals controlling gut epithelial turnover therefore represents an important step towards treating gut inflammatory diseases. The project takes advantage of the genetic amenability of the fruit fly to identify ISC niche-derived and systemic signals that control ISC activity and gut homeostasis.

While TNF signaling has mainly been studied in relation to its pathological role in driving inflammation-related metabolic disease, it is not clear whether TNF/TNF receptor (TNFR) signaling controls energy homeostasis in healthy individuals. We found that the highly conserved Drosophila TNFR, Wengen (Wgn), is required in the enterocytes (ECs) of the adult gut to restrict lipid catabolism, suppress immune activity, and maintain tissue homeostasis. Our findings suggest that Wgn/TNFR functions as an intersection between metabolism and immunity allowing pathogen-induced metabolic reprogramming to fuel the energetically costly task of combatting an infection (Loudhaief et al 2023).

To identify ISC niche-derived signals that are required for gut homeostasis and/or infection-induced regeneration, we selected all secreted peptides (app 800) and receptors (app 600) expressed in the adult gut, performed adult-specific knockdown of these in different gut resident cell populations using RNAis, and screened for increased sensitivity to oral infection with the mildly pathogenic bacteria Ecc15. Among the candidate genes identified in the primary screen, we conducted a secondary screen on the top 46 (secreted peptides) and 69 (receptor) hits, which were selected based on reproducibility and conservation in higher organisms. For this screen, we evaluated the effects of knocking down candidate genes on tissue turnover in homeostatic conditions (WPG I + III) and the proliferative response triggered by intestinal infection (II-III). Among our top candidate hits, we identified the two Drosophila activin ligands, Activin- (Act) and Dawdle (Daw) as key regulators of adult gut homeostasis. In short, we found that Act and Daw control distinct steps of intestinal stem cell (ISC)-to-enterocyte (EC) maturation and couple different environmental cues with the appropriate adaptive responses. While Act is highly upregulated in EBs in response to infection and required for the accelerated tissue turnover associated with regenerative growth, Daw responds to nutritional cues and plays an essential role in the adaptation of organ size to nutrient intake. This work was presented at several internal conferences (as selected talk) and published in Nature Communication in January 2024 (Christensen et al 2024).

Our screens also identified the highly conserved PDGF-VEGF-related ligand, Pvf1, and its receptor, PDGF-VEGF-related receptor, Pvr, as critical regulators ISC migration during gut regeneration. (WPGI-III). This work was presented as talks at multiple international conferences and will be submitted for publication within the next few months.

Finally, we could show that the highly conserved Drosophila TNFR, Wengen (Wgn), is required in the enterocytes (ECs) of the adult gut to restrict lipid catabolism, suppress immune activity, and maintain tissue homeostasis. Wgn limits autophagy-dependent lipolysis by restricting cytoplasmic levels of the TNFR effector, TNFR-associated factor 3 (dTRAF3), while it suppresses immune processes through inhibition of the dTAK1/TAK1-Relish/NF-κB pathway in a dTRAF2-dependent manner. This suggests that Wgn/TNFR functions as an intersection between metabolism and immunity allowing pathogen-induced metabolic reprogramming to fuel the energetically costly task of combatting an infection. Our work highlights the important protective and metabolic functions TNFRs might serve in the gut of healthy individuals and raises the question as to how the widespread use of anti-TNF therapies in the treatment of chronic inflammatory diseases, such as inflammatory bowels disease might affect these. This work was presented at several international conferences (as selected talk) and published in Science Advances last year (Loudhaief et al 2023).

The capacity of the intestine to adapt its size according to nutrient availability is highly conserved and particularly evident in animals with intermittent feeding patterns. Nevertheless, the mechanism underpinning nutrient-dependent adult gut resizing is not known. One of the most striking observations we made, was that this resizing is mainly controlled at the EB-to-EC differentiation step. Hence, while the pool of intestinal stem cells and mature cells (ECs and EECs) decrease upon nutrient deprivation, we observed an increase in the pool of EB progenitors, which is normalized upon refeeding. Hence, we speculate that the pool of stalled EBs provide a rapid source of ECs allowing quick expansion of the gut upon refeeding (Christensen et al 2023). This study provided the first example of a role of activin signaling in controlling gut homeostasis and points to a critical function of activins in controlling adult tissue homeostasis.

In our study on the role of Wgn/TNFR in controlling gut metabolism and immunity (WPG IV), we uncovered an unexpected TNF-independent role of Wgn in regulating the degradation of Drosophila TNFR-associated factor 3 (dTRAF3) (Loudhaief et al 2023). Intriguingly, another group subsequently published a role of Wgn in controlling the stability of receptor tyrosine kinases in the embryonic tracheal network, suggesting that Wgn/TNFR might have a more general role in controlling protein degradation. Our work opens the exciting possibility that other TNFRs might regulate protein localization and/or degradation and thereby regulate a broad spectrum of physiological processes independent of their canonical ligands.

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