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C. Leveau et al.
expressed genes, the most statistically significant differ- ences were observed in the group of downregulated genes (Figure 6B). To determine the functional profile of the dif- ferentially expressed genes, we performed GSEA for genes with a fold change ≥1.5. GO analysis of the identified gene signature revealed a significant enrichment of genes
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in three main categories. Two categories are related to chromatin organization/modification and DNA damage repair; this observation fits with our recent finding that Ttc7a is a chromatin-binding nuclear factor involved in chromatin compaction and nuclear organization28 (Figure 6C, D). Another category corresponds to genes involved
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Figure 6. Ttc7a deficiency results in reduced expression of endoplasmic reticulum stress response genes in hematopoietic stem cells. RNA sequencing was per- formed on 3-week old control (ctrl – black bars) and Ttc7a-deficient (fsn – red bars) hematopoietic stem cell (HSC) transcripts. (A) Heatmap of relative expression of differentially expressed genes (fold change ≥1.2) in Ttc7a-deficient HSC compared to control. (B) Volcano plot of differentially expressed genes (fold change ≥1.2) in Ttc7a-deficient HSC compared to control HSC showing the adjusted P-value (-log10) vs. fold change (log2). Upregulated and downregulated genes are shown in red and blue, respectively. Total numbers in each group are indicated in red and blue, respectively. (C-E) Enriched gene sets in Ttc7a-deficient HSC compared to control HSC, as determined by gene set enrichment analysis of differentially expressed genes (fold change ≥1.5). (F) Normalized expression of endoplasmic reticulum stress response genes downregulated in Ttc7a-deficient HSC (fold change ≥1,2) *P<0.05; **P<0.01; ****P<0.0001 (LimmaVoom analysis). NES: normalized enrichment score; FDR: false discovery rate; AU: arbitrary units.
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haematologica | 2020; 105(1)