Fig. 3: Characterization of HSPC composition and gene signatures in SCD patients vs HD cells by bulk and single-cell RNA-seq. | Nature Communications

Fig. 3: Characterization of HSPC composition and gene signatures in SCD patients vs HD cells by bulk and single-cell RNA-seq.

From: Severe inflammation and lineage skewing are associated with poor engraftment of engineered hematopoietic stem cells in patients with sickle cell disease

Fig. 3

a, b RNA-seq data were analyzed using DESeq2. We performed a two-sided hypergeometric test with MSigDB after correction for multiple hypothesis testing according to Benjamini and Hochberg on the DEG using Hallmark or custom genesets from published transcriptomic data24,66, 67 (Log2FC > 1.2, FDR < 0.05). a Top 10 enriched Hallmark genesets in SCD vs HDs HSPCs. b Top 5 enriched custom HSPC genesets in SCD vs HDs HSPCs. Red, upregulated genes in SCD and blue, downregulated genes in SCD in comparison with HDs. c, d Representation and quantification of modules of genesets activity with ROMA tool in individual HSPC samples using selected hallmark and gene ontology genesets (c) and custom genesets (d). Red arrows indicate inflammatory genesets. e Unsupervised analysis of 54,689 HSPCs and 15,961 genes from 3 HDs and 3 patients with SCD, represented as two-dimensional UMAP plots. Each individual cell in our dataset was annotated using the Cell-ID method and reference BM HSPC signatures24. HSC hematopoietic stem cell, HSC-enriched hematopoietic stem cell-enriched, MPP multipotent progenitors, MLP multipotent lymphoid progenitors, ImP1 & ImP2 immature myeloid progenitors, NeutroP neutrophil progenitors, MonoDCP monocyte and dendritic cell progenitors, BcellP B cell progenitors, MEP megakaryocyte and erythrocyte progenitors, EryP erythroid progenitors, MkP megakaryocyte progenitors, EoBasMastP eosinophil, basophil and mast cell progenitors, NA not annotated. f Proportion of the HSCs per individual. g Top 10 pathways (in terms of p-value, identified using a two-sided hypergeometric test, MSigDB and hallmark genesets) among the 280 DEGs identified with the MAST tool in SCD HSCs (n = 3) vs. HD HSCs (n = 3). In each pathway, genes that are upregulated in SCD (relative to HDs) are shown in red, and those that are downregulated in SCD are shown in blue. The false discovery rate (−log10(adjusted p-value)) is shown for each pathway. The numbers of upregulated and downregulated genes in each pathway are also shown. h, i Bar plots showing the percentages of NeutroP-MonoDCP (h) and MEP-MkP (i) in each individual.

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