Figure 5.
Claudin 1 is critical for the expression of antigen presentation–associated genes. (A) Representative FACS gating strategy used to perform bulkSeq of Cldn1+/+ and Cldn1−/− thymic DC1 lineage cells isolated from competitive BM chimera described in Fig. 3 D (n = 3 mice). Cells were gated as CD45.1+ (that included Cldn1+/+ DC1 lin.) or CD45.2+ (that included Cldn1−/−DC1 lin.). Both CD45.1+ and CD45.2+ cells were further gated as DC1, aDC1a, and aDC1b according to Fig. S2 A. DC1 lineage cells sharing the common origin (CD45.1+ or CD45.2+) were sorted into a common collection tube and sequenced. Sorting gates are highlighted by thick lines. (B) Volcano plot of bulkSeq analysis showing up- and downregulated genes in Cldn1−/− over Cldn1+/+ DC1 lineage cells. The threshold of P value adjusted after FDR correction is 0.05 and for log2 fold change is 0.5. The baseMean cutoff was set to 10. (C) Heat map showing relative expression of genes involved in MHCII presentation across individual sequenced samples. The heat map color scale corresponds to z scores of regularized log data values. The numbers below each column in the heat map correspond to three independent biological replicates, each derived from an individual mouse. (D) GSEA of “Antigen processing and presentation of peptide or polysaccharide antigen via MHC class II” pathway between Cldn1+/+ and Cldn1−/− DC1 lineage cells. (E) Heat map showing the relative expression of Cd207 and Cd36 genes in Cldn1+/+ and Cldn1−/− DC1 lineage cells. The heat map color scale corresponds to z scores of regularized log data values. The numbers below each column in the heat map correspond to three independent biological replicates, each derived from an individual mouse. (F) Frequency of DC1 lineage subsets within B220–CD11c+ cells from I-abfl/fl (control; solid circle) and XCR1iCreI-abfl/fl (empty circle) mice (mean ± SEM, n = 5–9 mice from two independent experiments). Statistical analysis in F was performed using unpaired, two-tailed Student’s t test, *P ≤ 0.05, **P ≤ 0.01, ****P < 0.0001. All mice were bred on the B6 background. Littermates were used as controls.

Claudin 1 is critical for the expression of antigen presentation–associated genes. (A) Representative FACS gating strategy used to perform bulkSeq of Cldn1+/+ and Cldn1−/− thymic DC1 lineage cells isolated from competitive BM chimera described in Fig. 3 D (n = 3 mice). Cells were gated as CD45.1+ (that included Cldn1+/+ DC1 lin.) or CD45.2+ (that included Cldn1−/−DC1 lin.). Both CD45.1+ and CD45.2+ cells were further gated as DC1, aDC1a, and aDC1b according to Fig. S2 A. DC1 lineage cells sharing the common origin (CD45.1+ or CD45.2+) were sorted into a common collection tube and sequenced. Sorting gates are highlighted by thick lines. (B) Volcano plot of bulkSeq analysis showing up- and downregulated genes in Cldn1−/− over Cldn1+/+ DC1 lineage cells. The threshold of P value adjusted after FDR correction is 0.05 and for log2 fold change is 0.5. The baseMean cutoff was set to 10. (C) Heat map showing relative expression of genes involved in MHCII presentation across individual sequenced samples. The heat map color scale corresponds to z scores of regularized log data values. The numbers below each column in the heat map correspond to three independent biological replicates, each derived from an individual mouse. (D) GSEA of “Antigen processing and presentation of peptide or polysaccharide antigen via MHC class II” pathway between Cldn1+/+ and Cldn1−/− DC1 lineage cells. (E) Heat map showing the relative expression of Cd207 and Cd36 genes in Cldn1+/+ and Cldn1−/− DC1 lineage cells. The heat map color scale corresponds to z scores of regularized log data values. The numbers below each column in the heat map correspond to three independent biological replicates, each derived from an individual mouse. (F) Frequency of DC1 lineage subsets within B220–CD11c+ cells from I-abfl/fl (control; solid circle) and XCR1iCreI-abfl/fl (empty circle) mice (mean ± SEM, n = 5–9 mice from two independent experiments). Statistical analysis in F was performed using unpaired, two-tailed Student’s t test, *P ≤ 0.05, **P ≤ 0.01, ****P < 0.0001. All mice were bred on the B6 background. Littermates were used as controls.

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