Figure 3. Critical role of Atg16L1 in the structure and transcriptional profile of Paneth cells.

a-d, EM of littermate WT (a, c) and Atg16L1^HM (b, d) Paneth cells (a, b: dotted lines denote individual cells, asterisk indicates normal progenitor cell; c, d: blue stars indicate normal mitochondria in WT Paneth cells and Atg16L1^HM progenitor cells, red diamonds indicate degenerating mitochondria, dotted Box shows normal Golgi compartments, and yellow asterisks indicate granules) (n = 3 mice/genotype). e, Mitochondrial integrity was quantified based on the percentage of the visible mitochondrial section displaying intact cisternae (n = 49 WT and 71 Atg16L1^HM cells). f, Enrichment of pathways associated with human orthologs mapped from genes differentially expressed in Atg16L1 deficient Paneth cells relative to WT cells, using the canonical pathway collection from MSigDB²⁴. The bar chart displays the negative log of the enrichment p-values for each pathway using the hypergeometric distribution (see methods). *denotes pathways found to be significantly enriched (p<0.05). Pathways with only one gene assigned were excluded from the chart. g, Chart of selected genes whose mRNA are enriched in either Atg16L1 deficient Paneth cells (baseline = WT Paneth cells) or Atg16L1 deficient thymocytes (baseline = WT thymocytes). N.S. = not significant. Scale bars: a-b, 10 μm; c-d, 500nm.