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Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies
Elisa ten Hacken, Rebecca Valentin, Fara Faye D. Regis, Jing Sun, Shanye Yin, Lillian Werner, Jing Deng, Michaela Gruber, Jessica Wong, Mei Zheng, Amy L. Gill, Michael Seiler, Peter Smith, Michael Thomas, Silvia Buonamici, Emanuela M. Ghia, Ekaterina Kim, Laura Z. Rassenti, Jan A. Burger, Thomas J. Kipps, Matthew L. Meyerson, Pavan Bachireddy, Lili Wang, Robin Reed, Donna Neuberg, Ruben D. Carrasco, Angela N. Brooks, Anthony Letai, Matthew S. Davids, Catherine J. Wu
Elisa ten Hacken, Rebecca Valentin, Fara Faye D. Regis, Jing Sun, Shanye Yin, Lillian Werner, Jing Deng, Michaela Gruber, Jessica Wong, Mei Zheng, Amy L. Gill, Michael Seiler, Peter Smith, Michael Thomas, Silvia Buonamici, Emanuela M. Ghia, Ekaterina Kim, Laura Z. Rassenti, Jan A. Burger, Thomas J. Kipps, Matthew L. Meyerson, Pavan Bachireddy, Lili Wang, Robin Reed, Donna Neuberg, Ruben D. Carrasco, Angela N. Brooks, Anthony Letai, Matthew S. Davids, Catherine J. Wu
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Research Article Hematology Therapeutics

Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies

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Abstract

The identification of targetable vulnerabilities in the context of therapeutic resistance is a key challenge in cancer treatment. We detected pervasive aberrant splicing as a characteristic feature of chronic lymphocytic leukemia (CLL), irrespective of splicing factor mutation status, which was associated with sensitivity to the spliceosome modulator, E7107. Splicing modulation affected CLL survival pathways, including members of the B cell lymphoma-2 (BCL2) family of proteins, remodeling antiapoptotic dependencies of human and murine CLL cells. E7107 treatment decreased myeloid cell leukemia-1 (MCL1) dependence and increased BCL2 dependence, sensitizing primary human CLL cells and venetoclax-resistant CLL-like cells from an Eμ-TCL1–based adoptive transfer murine model to treatment with the BCL2 inhibitor venetoclax. Our data provide preclinical rationale to support the combination of venetoclax with splicing modulators to reprogram apoptotic dependencies in CLL for treating venetoclax-resistant CLL cases.

Authors

Elisa ten Hacken, Rebecca Valentin, Fara Faye D. Regis, Jing Sun, Shanye Yin, Lillian Werner, Jing Deng, Michaela Gruber, Jessica Wong, Mei Zheng, Amy L. Gill, Michael Seiler, Peter Smith, Michael Thomas, Silvia Buonamici, Emanuela M. Ghia, Ekaterina Kim, Laura Z. Rassenti, Jan A. Burger, Thomas J. Kipps, Matthew L. Meyerson, Pavan Bachireddy, Lili Wang, Robin Reed, Donna Neuberg, Ruben D. Carrasco, Angela N. Brooks, Anthony Letai, Matthew S. Davids, Catherine J. Wu

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Figure 1

Aberrant splicing is a general property of CLL, which underlies sensitivity to splicing modulation.

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Aberrant splicing is a general property of CLL, which underlies sensitiv...
(A) Proportion of events within splicing categories of the 192 differential splice events based on analysis of RNA-seq data from 7 normal B cell samples and 22 CLL samples (13 CLL-SF3B1wt and 9 SF3B1mut). (B) Distribution of splice events in 22 CLL samples compared with 7 CD19+ cells based on Δ percent spliced in (ΔPSI) values versus negative logarithmic P values (–log10P) of all splicing changes. Pink and black dashed lines indicate thresholds of |ΔPSI| of 10% and FDR of 10% (i.e., –log10P = 1) for significant splice changes. Blue frequency bars indicate the number of significantly differential events in CLL as compared with normal B cells, of a total of 192. Light blue bars indicate nonsignificant events falling within the –10 < PSI < 10 interval. (C) PSI values of the 87 intron retention events within the 192 most differential splicing displayed in panel A. P value was calculated by Mann Whitney U test. (D) Total number of the top tenth percentile outlier splicing events across normal B cell and CLL samples, based on RNA-seq analysis. Reported P values were calculated by Welch t test with Bonferroni correction. (E) Pathway enrichment analysis by the Panther algorithm of the 192 most differential splicing events between CLL and normal B cells (black) and the CLL-specific splicing outliers represented in at least 7 of the 22 CLL samples (blue). Significantly enriched pathways within each category and respective –log10P values are indicated in the figure. (F) Percentage viability of CD19+ cells from 5 healthy donor PBMCs, 10 SF3B1wt CLL samples, and 10 SF3B1mut CLL samples after 8 hours of treatment with increasing concentrations of E7107 (1 nM to 1 μM). Reported P values were calculated by 1-way ANOVA with Scheffé’s correction.

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