Genetic alterations associated with drug resistance in agressive forms of CLL and Waldenstrom’s macroglobulinemia

Chronic lymphocytic leukemia (CLL), the most common adult leukemia in Western countries, is characterized by the expansion of mature CD5+ B cells in the blood, bone marrow, lymph nodes and spleen. CLL is an incurable disease with a heterogeneous clinical course. The prognosis depends on clinical staging and biological markers, including genetic aberrations. Our team focusses in the assessment of the gain of short arm of chromosome 2 (2p gain) and MYC and TP53 abnormalities, which are associated with poor prognosis.
We have initially demonstrated that 2p gain was associated with XPO1, TTC27, BCL11A, REL, AHSA2, and USP34 overexpression, and that XPO1 plays a pivotal role in drug resistance (Cosson et al., Leukemia 2017). We now unravel the specific role of these genes in CLL drug resistance in order to determine whether they cooperate with XPO1 in the apoptotic avoidance characterizing 2p. Our strategy involves deactivation (CRISPR-cas9 approach) and overexpression (classical dead-Cas9-VP64 transcriptional activation strategy) of these genes in various specific model cell lines. (Pr. Florence NGUYEN-KHAC leads this part of our research program).

MYC abnormalities (gain or translocation) are relatively less studied in CLL because of their rarity. Our aim is to provide a cytogenetic and molecular portrait of these high-risk CLL using next generation sequencing and optical genome mapping, and to evaluate the in vitro response to innovative drugs by classical flow cytometry approaches. (Pr. Florence NGUYEN-KHAC and Dr. Elise CHAPIRO are the responsible of this project).

Alteration of the TP53 gene in CLL is one of the strongest predictors of short survival to poor response to conventional therapy and is now part of the routine clinical diagnostic. In a more translational approach and given the clinical relevance of TP53 alterations, our team has recently developed an efficient and reliable p53 functional assay fully validated in a clinical prospective. This assay is applied in a large cohort of CLL containing different TP53 mutations in order to determine the prognostic and drug resistance impact of each mutation. We also work on CLL patients who present a dysfunctionality in the p53 programmed cell death (PCD) pathway without disruption in the TP53 gene, using drug-resistance tests and NGS to search for genetic alterations in the members of the p53-pathway. (Dr. Magali LE GARFF-TAVERNIER manages this part of our research program).

Waldenström’s Macroglobulinemia (WM) is a rare chronic B-cell lymphoproliferative disorder characterized by a wide clinical heterogeneity that is imperfectly captured by the various biological markers currently available. Recurrent cytogenetic and molecular abnormalities in WM include respectively 6q deletion and somatic mutations in MYD88, CXCR4, ARID1A, CD79B, SPI1 and TP53 genes, the last two being associated with poor prognosis but in single studies and limited series. Our project proposes an integrative analysis of cytogenetics, targeted NGS and IGHV repertoire in a clinically annotated cohort of more than 200 WM patients. We expect to confirm the poor prognosis associated with SPI1 mutation that we previously described and to identify new prognostic mutational markers. The long-term goal is to characterize the functional consequences and the drug resistance mechanisms of these abnormalities, which could be new therapeutic targets. (Dr. Damien ROOS-WEIL, Pr. Florence NGUYEN-KHAC, and Pr. Frédéric DAVI lead this part of our research program).