Low Expression of the CIITA Gene Predicts Poor Outcome in Diffuse Large B-Cell Lymphoma

Background

Despite better therapeutic options and improved survival of diffuse large B-cell lymphoma (DLBCL), 30-40% of the patients still experience relapse with a dismal prognosis. To identify biological correlates for poor survival, we compared differentially expressed genes between high-risk DLBCL patients, who had relapsed or remained in remission after dose-dense chemoimmunotherapy.

Design and methods

We performed genome-wide exon array analysis (Affymetrix Human Exon 1.0 ST) with 38 de novo high-risk (aaIPI>1) DLBCL patients less than 65 years old. The patients were treated in a Nordic phase II protocol with six courses of R-CHOEP-14 followed by systemic central nervous system prophylaxis with one course of high dose methotrexate and high dose cytarabine. We quantified the expression data by MEAP (Multiple Exon Array Preprocessing) algorithm and identified differentially expressed genes between the patients, who relapsed (n=9; poor prognosis group) or remained in long-term remission (n=29; good prognosis group). RNA sequencing and oligonucleotide-based microarray data from 92 (Cancer Genome Characterization Initiative, CGCI) and 233 (Lymphoma/Leukemia Molecular Profiling Project, LLMPP) DLBCL patients were utilized for validation. In both validation cohorts, the patients were treated with chemoimmunotherapy.

Results

Gene expression profiling (GEP) identified 215 differentially expressed genes (DEGs) between the good and poor prognosis groups. Of these, 41% were upregulated and 59% suppressed in the patients with poor prognosis. Pathway analyses indicated that the DEGs were enriched in many immune response related processes, such as the antigen processing and presenting pathway. Of note was the observation that major histocompatibility complex class II transactivator (CIITA) and selected human leucocyte antigen- (HLA) genes were significantly suppressed in the poor prognosis group. A correlation between CIITA and HLA gene expression levels was also observed. In Cox univariate analysis with continuous variables, low CIITA expression predicted poor overall survival (OS; p = 0.035). Five-year OS rates were 89% and 50% for the patients with high and low CIITA mRNA levels, respectively (p = 0.007). The prognostic impact of CIITA expression on survival was confirmed in independent CGCI (OS; p = 0.020, PFS; p = 0.002) and LLMPP validation cohorts (OS; p = 0.002, PFS data not available). In the CGCI cohort, the association of CIITA expression with survival was independent of IPI. Consistent with previous data, suppression of certain HLA-genes was also associated with poor outcome.

Conclusions

The results demonstrate that low CIITA expression is a novel independent predictor of poor survival in patients with DLBCL. The loss of CIITA offers, through the loss of MHC class II expression, a mechanism of immune escape and treatment resistance.