Figure 1.
Figure 1. Novel SF3B1 in-frame deletions found in CLL patients result in aberrant splicing. (A) DNA sequencing reads from 3 CLL patients are aligned to show SF3B1 in-frame deletions: CLL1, p.K700_V701delinsN (p.K700del); CLL2 and CLL3, p.Q698_K700delinsQ (p.Q698del). The schematic below shows the 3 nt and 6 nt deletions resulting in replacement of K700 and V701 with N and of Q698, Q699, and K700 with Q, respectively. The deletion is highlighted in a gray box. (B) Heat map representing z score normalized percent spliced in (PSI) of aberrant junctions previously identified in SF3B1-mutant CLL patient samples (n = 194). Sample columns are grouped into SF3B1 variants: SF3B1 wild type (WT; n = 5), SF3B1 p.K700E (n = 5), and SF3B1 deletion mutants (n = 3). (C) Sashimi plot showing aberrant 3′ ss usage (red) with respect to canonical splicing (light blue) of ZDHHC16 exons 9 to 10 in different CLL patient samples: K700del (CLL1), Q698del (CLL2 and CLL3), SF3B1 p.K700E, and SF3B1 WT. The aberrant junction PSI is given as a percentage in each condition. For SF3B1 p.K700E and SF3B1 WT, the average read density and PSI is plotted (n = 5, each). (D) Four SF3B1 hotspot-specific aberrant ss’s show linear correlation between mutation allele frequency (%) and ss usage (PSI). Colors for splicing markers: light green, MAP3K7; light blue, DYNLL1; gray, TMEM14C; purple, ZDHHC16. Shapes for SF3B1 mutation status: circle, WT; triangle, p.K700E; square, p.K700del; star, p.Q698del. (E) Homology model based on cryo-electron microscopy structure of Hsh155 (SF3B1 homolog in yeast) interacting with pre–messenger RNA (pre-mRNA) near the deletion site (K700 and Q698 represented as magenta spheres, PDB: 5GM6) and crystal structure of apo-SF3B1 (PDB: 5IFE) are shown in top panel. Homology modeling of SF3B1 in-frame deletions, K700del and Q698del, based on the crystal structure (PDB: 5IFE) are shown in the bottom panel. The affected amino acid side chains are represented in stick (magenta), rest of the protein (yellow), and pre-mRNA (gray) in illustration.

Novel SF3B1 in-frame deletions found in CLL patients result in aberrant splicing. (A) DNA sequencing reads from 3 CLL patients are aligned to show SF3B1 in-frame deletions: CLL1, p.K700_V701delinsN (p.K700del); CLL2 and CLL3, p.Q698_K700delinsQ (p.Q698del). The schematic below shows the 3 nt and 6 nt deletions resulting in replacement of K700 and V701 with N and of Q698, Q699, and K700 with Q, respectively. The deletion is highlighted in a gray box. (B) Heat map representing z score normalized percent spliced in (PSI) of aberrant junctions previously identified in SF3B1-mutant CLL patient samples (n = 194). Sample columns are grouped into SF3B1 variants: SF3B1 wild type (WT; n = 5), SF3B1 p.K700E (n = 5), and SF3B1 deletion mutants (n = 3). (C) Sashimi plot showing aberrant 3′ ss usage (red) with respect to canonical splicing (light blue) of ZDHHC16 exons 9 to 10 in different CLL patient samples: K700del (CLL1), Q698del (CLL2 and CLL3), SF3B1 p.K700E, and SF3B1 WT. The aberrant junction PSI is given as a percentage in each condition. For SF3B1 p.K700E and SF3B1 WT, the average read density and PSI is plotted (n = 5, each). (D) Four SF3B1 hotspot-specific aberrant ss’s show linear correlation between mutation allele frequency (%) and ss usage (PSI). Colors for splicing markers: light green, MAP3K7; light blue, DYNLL1; gray, TMEM14C; purple, ZDHHC16. Shapes for SF3B1 mutation status: circle, WT; triangle, p.K700E; square, p.K700del; star, p.Q698del. (E) Homology model based on cryo-electron microscopy structure of Hsh155 (SF3B1 homolog in yeast) interacting with pre–messenger RNA (pre-mRNA) near the deletion site (K700 and Q698 represented as magenta spheres, PDB: 5GM6) and crystal structure of apo-SF3B1 (PDB: 5IFE) are shown in top panel. Homology modeling of SF3B1 in-frame deletions, K700del and Q698del, based on the crystal structure (PDB: 5IFE) are shown in the bottom panel. The affected amino acid side chains are represented in stick (magenta), rest of the protein (yellow), and pre-mRNA (gray) in illustration.

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