Figure 3 – Tet1iKO ISCs upregulate absorptive enterocyte genes in conventional housing.

(A) scRNA-seq from CONV housed mice identifies 4 ISC subclusters. (B) IEC marker enrichment reveals higher expression of ISC markers Lgr5, Olmf4 and Sox9 in ISC3 and ISC4. ISC2 is enriched for Mki67, Dmbt1, Alpi, Aoc1, Fabp1, Sis and Muc2. ISC1 expresses TA-associated Dmbt1 over other markers. (C) Cluster proportion analysis reveals that a larger number of ISCs in Tet1iKO mice belong to ISC2. In CONV housing, UMAP for UCell gene signatures shows (D) enrichment for stem cell genes in ISC3 and ISC4, (E) homogenous expression of progenitor genes across ISC subclusters, and (F) a subtle enrichment of enterocyte genes in ISC2. (G) UCell gene signature enrichment is unchanged between Tet1iKO and control across all ISC subclusters for (G) stem cell genes and (H) progenitor genes, but (I) the enterocyte signature is enriched in Tet1iKO compared to control mice across all ISC clusters. (J) 4 ISC subclusters are also identified in HL housed mice. (K) ISC markers Lgr5, Olmf4, Sox9 and Muc2 are most enriched in ISC2, while ISC1 is enriched for Mki67, Dmbt1 and Muc2 expression. ISC3 is enriched for Dmbt1, Aoc1, Fabp1 and Sis. ISC4 expresses Lgr5, Sox9 and is enriched for Mki67 and Sis expression. (L) HL ISC subpopulation proportions are highly similar between Tet1iKO and control. (M) UMAP for UCell gene signatures shows enrichment for the stem cell signature over all 4 HL ISC subclusters, but predominantly in ISC2 and ISC4. (N) The progenitor signature is also detected broadly across all subclusters and enriched in ISC1, while (O) the enterocyte signature is not reliably detected in any of the HL ISC subclusters. Comparing differences in UCell gene signature scores shows no change between HL Tet1iKO and control ISCs for (P) stem cell, (Q) progenitor, or (R) enterocyte gene signatures.