LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium

Abstract

Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify regulators of neonatal intestinal epithelial development by testing a small library of epigenetic modifier inhibitors in Paneth cell–skewed organoid cultures. We found that lysine-specific demethylase 1A (Kdm1a/Lsd1) is absolutely required for Paneth cell differentiation. Lsd1-deficient crypts, devoid of Paneth cells, are still able to form organoids without a requirement of exogenous or endogenous Wnt. Mechanistically, we find that LSD1 enzymatically represses genes that are normally expressed only in fetal and neonatal epithelium. This gene profile is similar to what is seen in repairing epithelium, and we find that Lsd1-deficient epithelium has superior regenerative capacities after irradiation injury. In summary, we found an important regulator of neonatal intestinal development and identified a druggable target to reprogram intestinal epithelium toward a reparative state.

A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation

“…This pattern change was even more pronounced in SI crypt IECs from Villin -Cre+ Lsd1 f/f mice, which conditionally lack Lsd1 in IECs, compared to wild type (WT) littermates ( Figure 4D ). Similar gating has previously been associated with enteroendocrine cells and their progenitors (Sato et al, 2011 ), which thus fits with our previous observation that enteroendocrine progenitors such as Neurod1 and Neurog3 are upregulated in Villin -Cre+ Lsd1 f/f mice (Zwiggelaar et al, 2020 ). However, upon performing intracellular flow cytometry staining for the canonical tuft cell marker DCLK1, we found that also a DCLK1 hi population fell within this gate and is increased in Lsd1 -deficient crypts ( Figure 4E ).…”

“…Treatment with GSK-LSD1 markedly reduced gene expression of Paneth and goblet cell markers, but caused an increase in enteroendocrine and tuft cell marker genes, particularly Gfi1b ( Figure 4B ). This supports our recent work in which we found that Lysine-specific Demethylase 1A (LSD1, KDM1A) is required for Paneth cell differentiation and contributes to goblet cell differentiation (Parmar et al, 2020 ; Zwiggelaar et al, 2020 ). Paneth cells are commonly gated as SSC hi CD24+ population in flow cytometry (Sato et al, 2011 ).…”

A semi-automated organoid screening method demonstrates epigenetic control of intestinal epithelial differentiation

“…4d ). Similar gating has previously been associated with enteroendocrine cells and their progenitors 26 , which thus fits with our previous observation that enteroendocrine progenitors such as Neurod1 and Neurog3 are upregulated in Villin -Cre+ Lsd1 f/f mice 39 . However, upon performing intracellular flow cytometry staining for the canonical tuft cell marker DCLK1, we found that also a DCLK1 hi population fell within this gate and is increased in Lsd1 -deficient crypts ( Fig.…”

“…4b ). This supports our recent work in which we found that Lysine-specific Demethylase 1A (LSD1, KDM1A) is required for Paneth cell differentiation and contributes to goblet cell differentiation 39,40 . Paneth cells are commonly gated as SSC hi CD24+ population in flow cytometry 26 .…”

“…We recently demonstrated a central role of LSD1 in Paneth and goblet cell differentiation and maturation 39,40 . Here, we confirm the critical role of LSD1 for IEC lineage differentiation in an unbiased screen and in addition provide indications that instead of Paneth/goblet cells there is an expansion of DCLK1+ tuft cells that is associated with a CD24 high SSC low population by flow cytometry ( Fig.…”