RT Journal Article
SR Electronic
T1 Aberrant splicing in B-cell acute lymphoblastic leukemia
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 225136
DO 10.1101/225136
A1 Kathryn L. Black
A1 Ammar S. Naqvi
A1 Katharina E. Hayer
A1 Scarlett Y. Yang
A1 Elisabeth Gillespie
A1 Asen Bagashev
A1 Vinodh Pillai
A1 Sarah K. Tasian
A1 Matthew R. Gazzara
A1 Martin Carroll
A1 Deanne Taylor
A1 Kristen W. Lynch
A1 Yoseph Barash
A1 Andrei Thomas-Tikhonenko
YR 2017
UL http://biorxiv.org/content/early/2017/12/01/225136.abstract
AB Background Mutations in splicing factor (SF) genes cause myelodysplastic syndromes and chronic lymphocytic leukemia (CLL). While such mutations had not been found in B-cell acute lymphoblastic leukemia (B-ALL), we previously reported that alternative splicing of the CD19 transcript is a robust mechanism of resistance to CD19-directed immunotherapy in children with B-ALL. We thus hypothesized that additional mRNAs may be alternatively spliced in these leukemias.Results Using flow cytometry-based cell purification protocols, deep RNA sequencing (RNA-seq), and the MAJIQ algorithm, we compared transcriptomes of CD19+/CD34+ pro-B cells from normal bone marrow donors to 18 primary pediatric B-ALL samples. We found 4,000-5,000 differential local splice variations (LSV) per leukemia sample, with 279 LSVs in 241 genes differentially spliced in every B-ALL sample. The consistently mis-spliced genes were significantly enriched in the RNA splicing pathway components and encoded ~100 different SFs, many from the SRSF and hnRNP families. Since aberrant LSVs in hnRNPA1 mRNA were present in 100% of B-ALL samples, we knocked down this transcript in a B-lymphoblastoid cell line using siRNA and defined 213 robust hnRNPA1-dependent events. Nearly 30% of the hnRNPA1-dependent LSVs were detectable in B-ALL samples, with one of the affected genes being DICER1, which is commonly mutated or down-regulated in many hematologic malignancies and included in the COSMIC dataset. We next asked how many other COSMIC genes are affected by aberrant splicing. We discovered 81 LSVs (mainly hnRNPA1-independent) in 41 COSMIC genes, including FBXW7, which was alternatively spliced in all 18 primary B-ALL samples. We were able to confirm 77 out of 81 of these LSVs in at least one of the two large independent RNA-seq B-ALL datasets generated by the TARGET Consortium and St Jude Children's Research Hospital. In fact, the twenty most common B-ALL drivers showed much higher prevalence of aberrant splicing than of somatic mutations.Conclusions B-ALL has widespread changes in splicing, likely due to the aberrant exon usage by SFencoding transcripts. Aberrant splicing also affects most known B-ALL drivers, suggesting that this type of post-transcriptional regulation contributes to disease pathogenesis.