Figure 2. Transcriptional differences... | Rockefeller University Press

$Transcriptional differences between PC longevities in control subjects and PC specificities in CeD. For A–C, scRNA-seq analysis was performed by pooling all PCs from the two controls (CD2158 and CD2161) for which equal numbers of cells were sorted for each longevity phenotype (gated as in Fig. S1 C, right panel; in total, 162 short-, 160 intermediate-, and 194 long-lived PCs). Variation explained by sequencing library or patient was regressed out, while retaining variation explained by PC longevity. (A) UMAP projection based on the first five principal components (top) and individual principal components, showing variation explained by longevity. (B) FACS index-sorting values for cell surface markers CD19 and CD45 for sorted PCs from one of the controls (CD2158; top). Negative values were converted to 1 before plotting on a logarithmic scale. scRNA-seq expression of CD19, PTPRC (CD45), and CD27 are shown below. (C) Volcano plot (left) showing DEGs between the short- and long-lived PC populations in A and B. Mean expression level of DEGs of interest are shown (right), with dot sizes indicating fraction of cells with nonzero expression. (D) PCs from CeD patients were pooled together according to disease status (four UCeD patients, three TCeD patients) for scRNA-seq analysis. 606 TG2-specific, 132 DGP-specific, and 657 PCs of unknown specificity were included in the analysis for UCeD; 351 TG2-specific, 99 DGP-specific, and 384 PCs of unknown specificity were included for TCeD. Variation explained by patient (and sequencing library for TCeD) was regressed out, retaining variation explained by PC specificity. UMAP projections (left) of PCs from UCeD patients (top) and TCeD patients (bottom) are based on the first 10 (UCeD) or 5 (TCeD) principal components. The individual principal components (PC1 for UCeD, PC2 for TCeD) with the most variation explained by specificity or longevity are shown (right). (E) DEGs between all (top) or only short-lived (bottom) TG2-specific PCs and PCs of unknown specificity in the UCeD patients included in D. 437 TG2-specific and 383 PCs of unknown specificity were included in the analysis of short-lived PCs. (F) Mean expression levels of DEGs of interest between TG2- or DGP-specific PCs and PCs of unknown specificity in UCeD as identified in E. (G) Mean expression levels of DEGs of interest between TG2- or DGP-specific PCs and PCs of unknown specificity in the TCeD patients shown in D. 270 TG2-specific, 62 DGP-specific, and 229 PCs of unknown specificity were included in the analysis of short-lived PCs. (H) DEGs in short-lived TG2-specific PCs between UCeD (437 cells, four patients) and TCeD (270 cells, three patients). Mean expression levels of the most interesting genes are shown (right). (I) DEGs in short-lived DGP-specific PCs between UCeD (78 cells, two patients) and TCeD (62 cells, two patients).$

Figure 2.

Transcriptional differences between PC longevities in control subjects and PC specificities in CeD. For A–C, scRNA-seq analysis was performed by pooling all PCs from the two controls (CD2158 and CD2161) for which equal numbers of cells were sorted for each longevity phenotype (gated as in Fig. S1 C, right panel; in total, 162 short-, 160 intermediate-, and 194 long-lived PCs). Variation explained by sequencing library or patient was regressed out, while retaining variation explained by PC longevity. (A) UMAP projection based on the first five principal components (top) and individual principal components, showing variation explained by longevity. (B) FACS index-sorting values for cell surface markers CD19 and CD45 for sorted PCs from one of the controls (CD2158; top). Negative values were converted to 1 before plotting on a logarithmic scale. scRNA-seq expression of CD19, PTPRC (CD45), and CD27 are shown below. (C) Volcano plot (left) showing DEGs between the short- and long-lived PC populations in A and B. Mean expression level of DEGs of interest are shown (right), with dot sizes indicating fraction of cells with nonzero expression. (D) PCs from CeD patients were pooled together according to disease status (four UCeD patients, three TCeD patients) for scRNA-seq analysis. 606 TG2-specific, 132 DGP-specific, and 657 PCs of unknown specificity were included in the analysis for UCeD; 351 TG2-specific, 99 DGP-specific, and 384 PCs of unknown specificity were included for TCeD. Variation explained by patient (and sequencing library for TCeD) was regressed out, retaining variation explained by PC specificity. UMAP projections (left) of PCs from UCeD patients (top) and TCeD patients (bottom) are based on the first 10 (UCeD) or 5 (TCeD) principal components. The individual principal components (PC1 for UCeD, PC2 for TCeD) with the most variation explained by specificity or longevity are shown (right). (E) DEGs between all (top) or only short-lived (bottom) TG2-specific PCs and PCs of unknown specificity in the UCeD patients included in D. 437 TG2-specific and 383 PCs of unknown specificity were included in the analysis of short-lived PCs. (F) Mean expression levels of DEGs of interest between TG2- or DGP-specific PCs and PCs of unknown specificity in UCeD as identified in E. (G) Mean expression levels of DEGs of interest between TG2- or DGP-specific PCs and PCs of unknown specificity in the TCeD patients shown in D. 270 TG2-specific, 62 DGP-specific, and 229 PCs of unknown specificity were included in the analysis of short-lived PCs. (H) DEGs in short-lived TG2-specific PCs between UCeD (437 cells, four patients) and TCeD (270 cells, three patients). Mean expression levels of the most interesting genes are shown (right). (I) DEGs in short-lived DGP-specific PCs between UCeD (78 cells, two patients) and TCeD (62 cells, two patients).

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