A role of selective ER-phagy in intestinal homeostasis and inflammation?

Principal Investigator

Associated Doctoral Researcher

Associated Principal Investigator

Background and current state of research

In order for the cell to respond to changing demands (e.g. energy supply and environmental factors), but also to replace old and damaged organelles, each cell is capable of autophagy. This occurs via the formation of the autophagosome, from an isolation membrane, and its fusion with a lysosome.1 The endoplasmic reticulum (ER) is the largest intracellular endomembrane system and can be classed as the “protein machinery” of the cell.2 As the location of synthesis of surface-bound or excretory proteins, the ER is also responsible for the folding of these proteins into their tertiary structure. Proteins that are incorrectly or insufficiently folded are extracted and degraded (ER associated degradation (ERAD)).3 Disruption of ER function often leads to an accumulation of unfolded proteins, known as ER stress. If this occurs, the cell activates the unfolded protein response (UPR) to restore homeostasis and ensure cell survival.3–5 Persistent ER stress has been linked to several diseases such as diabetes, neurodegenerative disorders, cancer, but also inflammatory bowel diseases (IBD) such as Crohn’s Disease (CD) or Ulcerative Colitis (UC).3,6,7 Other than protein synthesis, the ER also plays a vital part in lipid synthesis and ion homeostasis.2 As such, the ER is subject to constant turnover to replace old and/or damaged ER, as well as being used as a source of energy (by proteolysis) during longer periods of hunger.8 Several ER-phagy receptors have been discovered in the past years, such as cell-cycle progression gene 1 (CCPG1) and reticulon 3 (RTN3).9

A mutation resulting in a loss-of-function of autophagy related 16-like 1 (ATG16L1 – a known risk gene for IBD) is associated with deregulation of ER function, as well as defective autophagy. ATG16L1 loss resulted in unrestricted IL-22 dependent IFN-I expression via cyclic guanoadenine synthase coupled with stimulator of IFN genes (cGAS-STING) (STING is coded for by TMEM173) dependent detection of cytosolic dsDNA.10,11 This excessive IFN-I response resulted in massive necroptosis in the intestinal epithelium when autophagy is impaired, e.g. in ATG16L1 deficiency, and thus promoted intestinal inflammation.11 As ER-phagy plays a role in both autophagy and ER-function, it is plausible that ER stress exacerbates in the situation of defective ER-phagy. This could mean that ER-phagy receptors may play a role in the IFN-I response, which has been shown to be dependent on ER-phagy.12 Autophagy defects and unresolved ER stress mostly affect secretory highly active cells, e.g. Paneth and goblet cells13, meaning that loss of an ER-phagy protein could disrupt cellular homeostasis, inducing cell death and subsequent inflammatory phenotypes.

Chronic inflammatory diseases are immune-related disorders with severe morbidity, which can only be ameliorated but generally not cured by life-long therapies, posing a major economic challenge to public health. IBD is an archetypic model for the interplay of environmental triggers (as nutrition, infections and toxic agents) and genetic factors, which regulate immune signals and epithelial integrity. A link between ER-phagy and IBD has not yet been discovered.

Our goals

In this thesis, I will therefore identify how the expression and activation of the ER-phagy protein reticulophagy regulator 1 (RETREG1) is regulated (aim 1) as well as its exact regulatory role in ER-phagy (aim 2) and whether ER-phagy is involved in intestinal homeostasis (aim 3). Furthermore, I will examine the direct effect of a loss of RETREG1 (conditional knockout) on subsequent intestinal inflammation and pathogen clearance in vitro and in vivo (aim 4).

How to get there

More information

  1. Glick, D., Barth, S., and Macleod, K. F. “Autophagy: cellular and molecular mechanisms,” The Journal of Pathology, V. 221, No. 1, 2010, pp. 3–12.
  2. Borgese, N., Francolini, M., and Snapp, E. “Endoplasmic reticulum architecture: structures in flux,” Current Opinion in Cell Biology, V. 18, No. 4, 2006, pp. 358–64.
  3. Tsai, Y. C., and Weissman, A. M. “The Unfolded Protein Response, Degradation from the Endoplasmic Reticulum, and Cancer,” Genes & Cancer, V. 1, No. 7, 2010, pp. 764–78.
  4. Grootjans, J., Kaser, A., Kaufman, R. J., et al. “The unfolded protein response in immunity and inflammation,” Nature Reviews Immunology, V. 16, No. 8, 2016, pp. 469–84.
  5. Oslowski, C. M., and Urano, F. “Measuring ER Stress and the Unfolded Protein Response Using Mammalian Tissue Culture System.” Methods in Enzymology, vol. 490. Elsevier, 2011. pp. 71–92.
  6. Tschurtschenthaler, M., Adolph, T. E., Ashcroft, J. W., et al. “Defective ATG16L1-mediated removal of IRE1α drives Crohn’s disease–like ileitis,” The Journal of Experimental Medicine, V. 214, No. 2, 2017, pp. 401–22.
  7. Adolph, T. E., Tomczak, M. F., Niederreiter, L., et al. “Paneth cells as a site of origin for intestinal inflammation,” Nature, V. 503, No. 7475, 2013, pp. 272–6.
  8. Hamasaki, M., Noda, T., Baba, M., et al. “Starvation Triggers the Delivery of the Endoplasmic Reticulum to the Vacuole via Autophagy in Yeast,” Traffic, V. 6, No. 1, 2005, pp. 56–65.
  9. Grumati, P., Dikic, I., and Stolz, A. “ER-phagy at a glance,” Journal of Cell Science, V. 131, No. 17, 2018, p. jcs217364.
  10. Barber, G. N. “STING: infection, inflammation and cancer,” Nature Reviews Immunology, V. 15, No. 12, 2015, pp. 760–70.
  11. Aden, K., Tran, F., Ito, G., et al. “ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS–STING,” The Journal of Experimental Medicine, V. 215, No. 11, 2018, pp. 2868–86.
  12. Moretti, J., Roy, S., Bozec, D., et al. “STING Senses Microbial Viability to Orchestrate Stress-Mediated Autophagy of the Endoplasmic Reticulum,” Cell, V. 171, No. 4, 2017, pp. 809-823.e13.
  13. Huang, G. “ER stress disrupts Ca2+-signaling complexes and Ca2+ regulation in secretory and muscle cells from PERK-knockout mice,” Journal of Cell Science, V. 119, No. 1, 2006, pp. 153–61.