Combatting ibrutinib and venetoclax resistance in MCL and CLL From CRISPR screens and genetic analyses towards improved treatment

Mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL) are mature B-cell Non-Hodgkin lymphomas characterized by accumulation of small B cells in the lymphoid organs. Although patient prognosis has been improved over the last decade by the development of targeted therapies, such as the BTK-inhibitor ibrutinib or the BCL2-inhibitor venetoclax, these malignancies are still considered to be incurable. A significant subset of patients is primary resistant or develops resistance upon prolonged treatment, highlighting the need for novel treatment strategies and better stratification of which patients will respond to which therapy.
In this thesis, we used functional genetic CRISPR-Cas9 knock-out screens to identify kinases potentially involved in resistance to ibrutinib and venetoclax. To combat ibrutinib resistance, we developed a loss-of-adhesion CRISPR-Cas9 screen, with which we identified several novel proteins potentially involved in BCR-controlled adhesion, such as PAK2 and CRKL. We validated these by genetic and/or pharmacological means.
To combat venetoclax resistance, we first reviewed the currently available evidence on the underlying mechanisms of resistance to venetoclax in MCL, and proposed rational combination therapies to overcome this resistance. Next, we performed a CRISPR-Cas9 venetoclax-sensitizer screen. We identified CK2 as major regulator of venetoclax resistance in MCL, and validated this in several MCL cell lines and primary samples. Lastly, by analyzing karyotypes of 895 treatment-naïve CLL patients, we identified that the presence of a complex karyotype is an adverse prognostic feature for venetoclax treatment. These findings provide novel insights in overcoming target therapy resistance in MCL and/or CLL patients, to improve their outcome.