Figure 2.
SF3B1mt clone-intrinsic dominance is associated with differential transcript splicing but not differential gene expression. (A) Distribution of scRNA-seq sampling times and experimental methods. (B-C) Uniform manifold approximation and projection (UMAP) of 10x Genomics-sequenced HSPCs (B) and TARGET-seq sequenced HSCs/MEPs (C). 10x HSPC subsets were annotated by comparing marker gene expression with existing literature data. The TARGET-seq annotation shown reflects the ground truth cell identification obtained from fluorescence-activated cell sorting purification. (D) Violin plots of common differentially expressed genes comparing month 118 and month 31 visits in the 10x HSC/MPP subset and between SF3B1 K666N and N626D-genotyped HSC in TARGET-seq. Bonferroni-adjusted P values for the respective comparison are shown below each violin plot. (E) dPSI values comparing SF3B1K666N and SF3B1N626D HSC PSIs against control PSIs (NBM, n = 3). Event types are annotated per color. The diagonal lines highlight events with absolute clone/clone dPSI of <10. (F) PSI values of mutation-biased cryptic splicing events in SF3B1N626D (left) and SF3B1K666N HSC (right). A cryptic event was considered mutation-biased if the other mutant clone’s dPSI was <2%. (G) GO enrichment analysis of mutation-biased cryptic spliced genes in SF3B1K666N and SF3B1N626D HSC. (H) Sashimi plots of cryptic splicing events in METTL3, NCBP2, and SNW1, 3 of 4 genes associated with RNA splicing in the GO enrichment analysis; and RIPOR1 and FTCDNL1, examples of K666N-biased splicing events. The predicted molecular consequences of the cryptic sites are annotated below the corresponding sashimi plots. A3SS, alternative 3′ splice site; A5SS, alternative 5′ splice site; CLP, common lymphoid progenitors; dPSI, percent spliced-in difference; EryP: erythroid progenitors; GO, Gene Ontology; Ly, lymphoid; MkP, megakaryocyte progenitors; MPP, multipotent progenitor; MPD, months post diagnosis; MXE, mutually exclusive isoform usage; NBM, normal BM; RI, intron retention; scRNA-seq, single-cell RNA sequencing; SE, exon skipping.

SF3B1mt clone-intrinsic dominance is associated with differential transcript splicing but not differential gene expression. (A) Distribution of scRNA-seq sampling times and experimental methods. (B-C) Uniform manifold approximation and projection (UMAP) of 10x Genomics-sequenced HSPCs (B) and TARGET-seq sequenced HSCs/MEPs (C). 10x HSPC subsets were annotated by comparing marker gene expression with existing literature data. The TARGET-seq annotation shown reflects the ground truth cell identification obtained from fluorescence-activated cell sorting purification. (D) Violin plots of common differentially expressed genes comparing month 118 and month 31 visits in the 10x HSC/MPP subset and between SF3B1 K666N and N626D-genotyped HSC in TARGET-seq. Bonferroni-adjusted P values for the respective comparison are shown below each violin plot. (E) dPSI values comparing SF3B1K666N and SF3B1N626D HSC PSIs against control PSIs (NBM, n = 3). Event types are annotated per color. The diagonal lines highlight events with absolute clone/clone dPSI of <10. (F) PSI values of mutation-biased cryptic splicing events in SF3B1N626D (left) and SF3B1K666N HSC (right). A cryptic event was considered mutation-biased if the other mutant clone’s dPSI was <2%. (G) GO enrichment analysis of mutation-biased cryptic spliced genes in SF3B1K666N and SF3B1N626D HSC. (H) Sashimi plots of cryptic splicing events in METTL3, NCBP2, and SNW1, 3 of 4 genes associated with RNA splicing in the GO enrichment analysis; and RIPOR1 and FTCDNL1, examples of K666N-biased splicing events. The predicted molecular consequences of the cryptic sites are annotated below the corresponding sashimi plots. A3SS, alternative 3′ splice site; A5SS, alternative 5′ splice site; CLP, common lymphoid progenitors; dPSI, percent spliced-in difference; EryP: erythroid progenitors; GO, Gene Ontology; Ly, lymphoid; MkP, megakaryocyte progenitors; MPP, multipotent progenitor; MPD, months post diagnosis; MXE, mutually exclusive isoform usage; NBM, normal BM; RI, intron retention; scRNA-seq, single-cell RNA sequencing; SE, exon skipping.

Close Modal
This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal