CARD11 gain of function upregulates BCL2A1 expression and promotes resistance to targeted therapies combination in B-cell lymphoma

Abstract

Strategy combining targeted therapies is effective in B-cell lymphomas such as mantle cell lymphoma (MCL), but acquired resistances remain a recurrent issue. Herein, we performed integrative longitudinal genomic and single-cell RNA-seq analyses of MCL patients treated with targeted therapies against CD20, BCL2 and BTK (i.e., OAsIs trial). We revealed the emergence of subclones with a selective advantage against OAsIs combination in vivo and showed that resistant cells were characterized by BCR-independent overexpression of NFkB1 target genes, especially due to CARD11 mutations. Functional studies demonstrated that CARD11 gain of function not only resulted in BCR independence, but also directly increase the transcription of the antiapoptotic BCL2A1, leading to venetoclax and OAsIs combination resistance. Based on the transcriptional profile of OAsIs-resistant subclones, we designed a 16-gene resistance signature that was also predictive for MCL patients treated with conventional chemotherapy, underlying a common escape mechanism. Among druggable strategies to inhibit CARD11-dependent NFkB1 transduction, we evaluated the selective inhibition of its essential partner MALT1. We demonstrated that MALT1 protease inhibition led to the reduction of genes involved in OAsIs resistance, including BCL2A1. Consequently, MALT1 inhibition induced synergistic cell death in combination with BCL2 inhibition, irrespective of CARD11 mutational status, both in vitro and in vivo. Taken together our study identified mechanisms of resistance to targeted therapies and provided a novel strategy to overcome resistance in aggressive B-cell lymphoma.

Chimeric and mutant CARD9 constructs enable analyses of conserved and diverged autoinhibition mechanisms in the CARD-CC protein family

“…CARD11 was the first CARD-CC family member where activating mutations were found, which cause spontaneous NF-κB activation and result in BENTA disease or B cell lymphoma [53]. Some of these activating mutations in CARD11 — for example CARD11 G123D [45,54], CARD11 L232LI [55,56], or CARD11 S250P [44] (Fig. 2B) — are mutated in residues that are conserved in several CARD-CC paralogs (Fig.…”

Targeting BTK in B Cell Malignancies: From Mode of Action to Resistance Mechanisms

“…Recently, whole-exome sequencing of MCL samples has revealed recurrent mutations in various genes, including those already known to be mutated in MCL, such as ATM , MEF2B , and KMT2D [ 92 ]. Furthermore, this approach has identified novel mutated genes, including CARD11 , encoding a scaffold protein required for BCR-induced NF-κB activation [ 92 , 93 ]. CARD11 mutations were found in 5-15% of additional MCL cases and, when overexpressed in vitro, conferred resistance to ibrutinib and lenalidomide, indicating continuous activation of the NF-κB pathway, irrespective of BTKi ( Figure 1 ) [ 92 ].…”

Sending positive signals and good (calcium) vibes

“…These mutations can enhance proximal BCR signaling ( Mandato et al, 2023 ), which may suffice to extend that “primed” state. Finally, CARD11 mutations in a fraction of ABC-DLBCL ( Lenz et al, 2008 ) are known to drive increased expression of BCL2A1 ( Decombis et al, 2023 ), the anti-apoptotic factor engaged by SOCE and reinforced by CD40 stimulation ( Basso et al, 2004 ) that Yada et al (2024) showed can rescue high-affinity Stim1/2 null cells. Thus, predictably, the mutational repertoire of B-NHLs may be peppered with genes encoding for previously unknown second signals.…”