CTPS1 acts as a prognostic biomarker and therapeutic target in mantle cell lymphoma

Abstract

Introduction: Mantle cell lymphoma (MCL) represents 6 to 8% of non-Hodgkin’s lymphoma with generally poor prognosis. Cytidine triphosphate synthase 1 (CTPS1) is a critical regulatory enzyme in cytidine metabolism, catalyzing the rate-limiting step in de novo CTP synthesis. Herein, we aim to investigate the clinical significance and functional mechanisms of CTPS1 in MCL patients. Methods: Lymph node, bone marrow biopsy, peripheral blood specimens and MCL cell lines were utilized as models. Liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS)-based analysis was performed to measure the steady-state level of metabolites. GSE93291 dataset and immunohistochemistry (IHC) staining were utilized to determine the relationship between expression levels of CTPS1 and patient outcome. CRISPR/Cas9 editing was employed to engineer the loss-of-function models of CTPS1 and other key enzymes involved in CTP synthesis. Results: Metabolic Profiling revealed dramatically aberrant cellular abundance of metabolic intermediates in the CTP synthesis pathway (Figure 1A). For GSE93291 analysis, a nucleotide metabolism related prognostic model was established by bioinformatic analysis and CTPS1 was screened out by highest regression coefficient (Figure 1B). IHC staining of CTPS1 in 105 MCL tissues confirmed that elevated CTPS1 expression was significantly associated with poor PFS (P = 0.038) and OS (P = 0.001) in MCL patients (Figure 1C-D). Multivariate Cox regression analysis showed that high CTPS1 expression was an independent prognostic indicator of both PFS and OS. CTPS1 depletion significantly impaired outgrowth and increased apoptosis of MCL cells, suggesting that CTPS1 is the major isozyme important for MCL survival (Figure 1E-F). In primary tumor samples, MYC protein levels were significantly correlated with CTPS1 protein levels (P < 0.001, R = 0.638). MYC knockout blocked CTPS1 mRNA and protein expression prior to induction of cell death, suggesting a requisite role of MYC in CTPS1 transcription regulation (Figure 1G). Remarkably, TP53 aberrant and ibrutinib-resistant MCL cells rely on cytidine metabolism (Figure 1H). Genetic or chemical inhibition (3-deazauridine) of CTPS1 reversed poor responsiveness of MCL cell lines to ibrutinib (Figure 1I). Cytidine level was significantly increased in TP53-deficient MCL cells and the effect of CTPS1 inhibition was independent of TP53 status (Figure 1K). Gene set enrichment analysis of RNA-sequencing revealed that CTPS1 inhibition induced DNA damage and apoptosis. Moreover, CTPS1 inhibition caused cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) activation, which triggered innate immune pathway, leading to cells growth inhibition (Figure 1L). Keywords: Aggressive B-cell non-Hodgkin lymphoma, Diagnostic and Prognostic Biomarkers, Metabolism No conflicts of interests pertinent to the abstract.