CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival

M T Forster,J P Steinbach,S Stefanović,S Bernatz,J Zinke,F Thorsen,J Wischhusen,M Mittelbronn,P N Harter,K H Plate,H M Kvasnicka,P S Zeiner,A Muller,J Tichy,D J Kowalewski,B Weide,A Berger,R Beschorner,M W Ronellenfitsch

doi:10.1186/s40478-018-0521-5

Abstract

Despite multidisciplinary local and systemic therapeutic approaches, the prognosis for most patients with brain metastases is still dismal. The role of adaptive and innate anti-tumor response including the Human Leukocyte Antigen (HLA) machinery of antigen presentation is still unclear. We present data on the HLA class II-chaperone molecule CD74 in brain metastases and its impact on the HLA peptidome complexity.We analyzed CD74 and HLA class II expression on tumor cells in a subset of 236 human brain metastases, primary tumors and peripheral metastases of different entities in association with clinical data including overall survival. Additionally, we assessed whole DNA methylome profiles including CD74 promoter methylation and differential methylation in 21 brain metastases. We analyzed the effects of a siRNA mediated CD74 knockdown on HLA-expression and HLA peptidome composition in a brain metastatic melanoma cell line.We observed that CD74 expression on tumor cells is a strong positive prognostic marker in brain metastasis patients and positively associated with tumor-infiltrating T-lymphocytes (TILs). Whole DNA methylome analysis suggested that CD74 tumor cell expression might be regulated epigenetically via CD74 promoter methylation. CD74high and TILhigh tumors displayed a differential DNA methylation pattern with highest enrichment scores for antigen processing and presentation. Furthermore, CD74 knockdown in vitro lead to a reduction of HLA class II peptidome complexity, while HLA class I peptidome remained unaffected.In summary, our results demonstrate that a functional HLA class II processing machinery in brain metastatic tumor cells, reflected by a high expression of CD74 and a complex tumor cell HLA peptidome, seems to be crucial for better patient prognosis.

Highlights

Brain metastases (BM) are the most frequent brain tumors in humans
High CD74 expression on tumor cells was associated with prolonged patient overall survival after BM surgery in the total cohort as well as in our largest subcohorts of BM deriving from NSCLC and melanoma (Fig. 1d)
CD74 expression in tumor cells was not associated with clinical parameters such as Karnofsky Performance Status (KPS) or in case of melanoma the Graded Prognostic Assessment (GPA) Score (Additional file 1: Figure S1)

Summary

Introduction

Brain metastases (BM) are the most frequent brain tumors in humans. Despite multimodal therapies including radio-chemotherapy, neurosurgery and/or stereotactic irradiation patient survival is still poor, often not exceeding 6–12 months [3, 43]. Frenard and colleagues showed that ipilimumab treatment (CTLA-4-dependent checkpoint-inhibitor) failed to prevent metastases formation in the per se immune privileged environment of the brain in patients suffering from metastatic melanoma [12] despite a potentially enhanced systemic immune response. It has been described that the mutational load of metastatic melanomas predicts a better response to CTLA-4 blockade [41]. Even across different tumor entities, the response to immunotherapy is associated with mutational load as presented in humans via human leukocyte antigen (HLA) molecules [2]. This indicates that the mutational landscape presented via HLA molecules might be crucial for an adequate immune and therapy response

Methods

Results

Conclusion