<scp>DNA</scp> repair in diffuse large B‐cell lymphoma: a molecular portrait (2014)

Diffuse large B-cell lymphoma (DLBCL) accounts for 30–40% of adult non-Hodgkin lymphomas. Most DLBCL patients achieve long-term remission after treatment, but a third relapse after conventional Rituximab (R)-based chemotherapy regimens, such as CHOP (cyclophosphamide, doxorubicin, vincristine and prednisone) (Siegel et al, 2012). Cancer cells are exposed to chronic replication stress, which impedes the duplication of their genome and induces mitotic catastrophe (Shaheen et al, 2011). Functional DNA repair pathways are therefore important for the survival of cancer cells. This dependence can be exploited therapeutically to hamper repair of the intrinsic DNA damage occurring during replication or to exacerbate DNA damage induced by chemotherapy (Shaheen et al, 2011). Furthermore, high-risk DLBCL patients overexpress genes potentially involved in resistance to CHOP-based regimens, such as genes of the nucleotide excision repair (NER) pathway (Bret et al, 2012, 2013). This study aimed to identify deregulated DNA repair pathways in DLBCL tumour samples in order to develop novel therapeutic strategies that exploit the concept of synthetic lethality and overcome drug resistance. Gene expression microarray data from two independent cohorts of patients diagnosed with DLBCL were used (n = 233 treated with R-CHOP; n = 181 treated with CHOP) (Lenz et al, 2008). (Gene Expression Omnibus; accession number GSE10846). A list set of 176 genes involved in six major DNA repair pathways [base excision repair (BER), NER, mismatch repair (MMR), homologous recombination repair (HRR), non-homologous end joining (NHEJ) and FANC pathways] was defined using the REPAIRtoire database (http://repairtoire.genesilico.pl) and review of the literature (Table SI). The Maxstat R function and Benjamini Hochberg multiple testing correction showed that 126 out of the 176 genes have a prognostic value (92 genes with poor and 34 with good prognostic values) (Table SII). For each pathway, a gene expression profile (GEP)-based risk score was created as the sum of the beta coefficients weighted by ±1 according to the patient signal above or below the probe set Maxstat value as previously reported (Kassambara et al, 2012). For each pathway, patients were ranked according to increased prognostic score and for a given score value X, the difference in survival of patients with a prognostic score ≤X or >X was computed using Maxstat analysis. High FANC, NER, HRR, BER, NHEJ and MMR scores were significantly associated with poor prognosis in the two cohorts of patients (Figure S1A–F and Table SIII–SVIII). The NER, HRR, BER, NHEJ or MMR scores were significantly higher (P < 0·01) in the activated B-cell like (ABC) molecular subgroup compared to the germinal centre B cell (GCB) subgroup whereas no significant differences were observed for FANC score (Figure S2). Interestingly, FANC, NER, HRR, BER, NHEJ and MMR scores had prognostic value in both GCB and ABC molecular subgroups (Figure S3). Cox analysis was used to determine whether the different DNA repair pathway scores provided additional prognostic information compared to previously identified poor outcome-related factors. When all parameters were tested together, only the gene expression-based risk score (GERS), FANC, NHEJ and MMR scores maintained prognostic value (Table SIX). Given that the FANC, NHEJ and MMR scores displayed independent prognostic information, these three DNA repair scores were combined to create a new DNA repair score. Using Maxstat, the RCHOP cohort was classified into three groups according to the combined DNA repair score. Groups I (low DNA repair score; n = 40) and II (intermediate DNA repair score; n = 144) had not reached a median overall survival (OS) although Group I had significantly better OS than Group II (P = 0·0005). Group III (high DNA repair score; n = 48) had the worst prognostic value with a median OS of 13·9 months (Fig 1A): 28% of Group III patients were in the low International Prognostic Index (IPI) risk group, 33% were low-intermediate IPI, 13% were high-intermediate IPI and 26% were high risk IPI; 58% of patients were ABC subtype, 33% in GCB and 9% were unclassified. The prognostic value of the DNA repair score was validated in the CHOP cohort (Figure S4). Comparing the DNA repair score with other poor outcome-related factors, such as GERS score, GCB or ABC subtype and the IPI in multivariate COX analysis, only DNA repair score retained prognostic value (Table 1). We investigated the prognostic value of the DNA repair score for subgroups of DLBCL patients defined by IPI. DNA repair score allowed all IPI subgroups to be divided into three groups (Fig 1B). The prognostic value of the DNA repair score was not significant in the low IPI risk group (P = 0·1) but segregated DLBCL patients with low-intermediate, high-intermediate and high IPI risk into three significantly different prognostic groups (P = 0·01, P = 0·03 and P = 0·01 respectively) (Fig 1B). Several DNA repair inhibitors are being tested in clinical cancer trials (Shaheen et al, 2011). DLBCL treatments include cyclophosphamide, a nitrogen mustard derivate that induces interstrand crosslinks (ICLs), and doxorubicin, a DNA topoisomerase inhibitor that induces DNA double-strand breaks, DNA adducts and formaldehyde-dependent ICL formation (Bret et al, 2013). Inhibiting DNA repair is a promising strategy to improve the efficacy of genotoxic drugs and overcome drug resistance (Curtin, 2013). Our data support the view that inhibitors of DNA damage signalling and DNA repair have potential therapeutic interest in DLBCL. Despite overall improvements in the treatment of DLBCL, including the use of rituximab, approximately one-third of patients fail to achieve complete remission or experience relapse. This remains a major cause of morbidity and mortality. The DNA repair scores could be useful to identify high-risk DLBCL patients and define the best DNA repair inhibitor to employ in combination with conventional treatment. Accordingly, it will be important to evaluate the association of DNA repair scores with event-free survival or time to first relapse. Furthermore, these DNA repair scores could be useful at different times of treatment, particularly at relapse, to define targeted therapies that have greater effectiveness and render resistant tumours responsive to treatment. Recent data indicate that DLBCL relapse may result from multiple different evolutionary mechanisms (Redmond et al, 2013). The DNA repair scores could be valuable for adapting targeted treatment according to the drug resistance mechanisms selected during clonal evolution. As GEP is not included in the current routine diagnostic work-up, efforts should be made to identify substitutes involving immunohistochemistry (Curtis et al, 2010) or quantitative measurement of alterations in DNA repair pathways using single cell network profiling by flow cytometry (Rosen et al, 2014). Furthermore, understanding of the functional role of these DNA repair pathways in the pathogenesis and drug resistance of DLBCL is needed. These advances may limit the side effects of treatment, improving compliance with dosing regimens and overall quality of life. This work was supported by grants from ANR emergence (ETTMM), FEDER (141786 & 42667) and Languedoc Roussillon CRLR (R14026FF). CB performed research, bioinformatic studies and participated in the writing of the paper. BK participated in the research and in the writing of the paper. GC participated in clinical data analysis and participated in the writing of the paper. JFS participated in the writing of the paper. AC participated in the research and in the writing of the paper. PP participated in the research and in the writing of the paper. JM supervised the research, bioinformatic studies and the writing of the paper. The authors have no conflicts of interest to disclose. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.