Figure 5 from Engineering Oncogenic Hotspot Mutations on SF3B1 via CRISPR-Directed PRECIS Mutagenesis

SF3B1 mutation induces LOY in both cell lines and CLL patient samples. A, DEG analysis of HG-3 SF3B1 mutant vs. WT cell lines. Log₂FC ≥1 and ≤−1 and adjusted P value <0.05 chosen as statistical cutoffs. B, Schematic depiction of chromosome (top) Y and (bottom) 12 with PCR targets and loci indicated. C, PCR of Y chromosome genes in genomic DNA of HG-3 SF3B1 WT and mutant cell lines. D, Top, Timeline for the PRECIS engineering of SF3B1 K700E and (bottom) PCR of Y chromosome genes in HG-3 genomic DNA at different time points in the PRECIS engineering process. Clones 65-8 (blue) and 76-13 (red) became the final isogenic HG-3 SF3B1 WT and mutant cell line, respectively. E, Y chromosome gene signature score for 43 Y chromosome genes in SF3B1 WT and mutant male CLL patient samples. A Mann–Whitney test was used (***, P ≤ 0.001). F, DEG analysis of 43 Y chromosome genes comparing SF3B1 mutant vs. WT male CLL patient samples. One-tailed t-test was performed with log₂FC ≥0 as the null hypothesis and log₂FC < 0 as the alternative hypothesis. G, TPM expression for different Y chromosome genes in SF3B1 WT and mutant male CLL patient samples. Mann–Whitney test was used (****, P ≤ 0.0001; ***, P ≤ 0.001; *, P ≤ 0.05). Some figures created with BioRender.com.