TRAF3 Alterations Identify a Subgroup of Patients with Adverse Clinical Outcome and Induce Metabolic Reprogramming in Chronic Lymphocytic Leukemia

The TNF receptor-associated factor3 (TRAF3) gene located in 14q32 is frequently altered by deletion and/or mutation in multiple myeloma, lymphoma and other B-cell malignancies such as chronic lymphocytic leukemia (CLL). TRAF3 is a negative regulator of the non-canonical NF-KB signaling, and recent data uncovered additional functions of this gene in inflammation, antiviral immunity or cellular metabolism. Nevertheless, the biological and clinical significance of TRAF3 alterations in CLL is unknown. For that, the aim of this study was to assess the clinical impact of TRAF3 alterations in a CLL cohort as well as its biological role in CLL pathogenesis through CRISPR/Cas9-generated models.

TRAF3 alterations (mutations and copy number variations-CNVs) were assessed by NGS in our previously published cohort of 340 CLLs (Pérez Carretero, AJH 2022). A total of 14 patients exhibited a TRAF3 CNV loss, and 10 of them showed additional TRAF3 loss-of-function mutations, indicating a biallelic inactivation of this gene in CLL. Interestingly, the presence of TRAF3 alterations was significantly associated with shorter time to first treatment (6 vs 75 months, p<0.001), being an independent risk factor in the multivariate analysis (p=0.029).

To further investigate the biological role of TRAF3, we used the CRISPR/Cas9 system to model TRAF3 loss-of-function mutations in the CLL-derived cell line PGA1, and characterized these cells by transcriptomics, metabolomics and functional studies. RNA-seq analyses identified 54 dysregulated genes enriched in pathways such as NIK/NF-kB signaling (FDR=0.029). Concretely, NIK (a direct target of TRAF3-mediated degradation) was significantly upregulated (Q<0.001) in TRAF3^mut clones, which correlated with a higher nuclear activity of the non-canonical NF-kB transcription factors p52 (p=0.05) and RelB (p=0.02). Moreover, we validated these results in primary CLL cells (n=15; 3 TRAF3^mut cells). Besides, PGA1-TRAF3^mut cells showed increased levels of BAX (p=0.05) and more sensitivity to venetoclax (IC₅₀ 3.1 vs 13.8μM, p=0.003).

In the metabolomic study, we found an enrichment of metabolites involved in Warburg effect, citric acid cycle (TCA) and glutamate metabolism (FDR<0.001, 0.003, 0.1 resp.), with significant higher levels of α-ketoglutarate (TCA intermediate synthesized from glutamate), pyruvate and lactate (products of glycolysis) (p<0.001, p<0.001, p=0.002) in PGA1-TRAF3^mut cells. To better analyze their metabolic specificities, we evaluated the mitochondrial oxygen consumption rate (OCR) extracellular acidification (ECAR) and cell viability at basal state and in response to metabolic inhibitors. Of note, PGA1-TRAF3^mut cells exhibited distinct mitochondrial characteristics: higher basal and maximal respiration levels and a more important spare capacity and generation of ATP-linked to mitochondrial respiration. Glycolysis and glycolytic reserve were also enhanced in the TRAF3^mut cells. In this way, they were more sensitive to 2-deoxy-D-glucose (glucose uptake inhibitor), and more resistant to oxamate (lactate-dehydrogenase inhibitor, marker of anaerobic glycolysis). Overall, these results indicate, unlike WT, TRAF3^mut cells instead utilize a mitochondrial glycolytic metabolism.

Surprisingly, by using UK5099 (inhibitor of the mitochondrial pyruvate transporter that regulates mitochondrial glycolysis) mutant cells showed higher maximal respiration levels than WT, suggesting a metabolic reprogramming towards an alternative metabolic way fueling mitochondrial metabolism. We therefore tested the effect of C968 (glutaminolysis inhibitor) and we found that TRAF3^mut cells were also more resistant to this drug, what reveals a specific metabolic plasticity (mitochondrial glycolysis/glutaminolysis) in the PGA1-TRAF3^mut cells that does not exist in the WT. Interestingly, the combined treatment (UK5099 and C968) induced more cell death in the TRAF3^mut than in the WT cells (p=0.03), suggesting a new potential opportunity to treat patients with TRAF3 alterations.

In conclusion, TRAF3 deficiency appeared to be an independent prognostic factor of time to first treatment in CLL. This alteration results in a non-canonical NF-KB activation and in a metabolic reprogramming towards an enhanced mitochondrial glycolysis and glutaminolysis, which could be potentially targetable in CLL patients.

Fund.: PI21/00983 FI19/00191 FEHH

Hernández-Rivas:Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; GSK: Consultancy, Honoraria; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Support, Speakers Bureau; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research support, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Support; Janssen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Roche: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Abbvie: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AstraZeneca: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Beigene: Membership on an entity's Board of Directors or advisory committees; Lilly: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Rovi: Membership on an entity's Board of Directors or advisory committees; Incyte: Membership on an entity's Board of Directors or advisory committees.