Molecular Features of Primary Central Nervous System Lymphoma in a Large Tissue Microarray
Authors: Villa Diego , Slack Graham W , Al-Moosawi Muntadhar , Ben-Neriah Susana , Shenkier Tamara , Connors Joseph M. , Sehn Laurie H , Savage Kerry J , Scott David W. , Steidl Christian , Gascoyne Randy D. , Tan King 
Published: October 2019

Abstract
Background
The pathogenesis of primary central nervous system lymphoma (PCNSL) remains poorly understood. The objective of this study was to evaluate the distribution and prognostic impact of a broad range of molecular attributes in a large tissue microarray (TMA) from immunocompetent patients with PCNSL.
Methods
Patients with PCNSL diagnosed during 1998 - 2010 were identified using the BC Cancer Lymphoid Cancer clinical and pathology databases. Archival formalin-fixed, paraffin-embedded diagnostic biopsy tissue was retrieved, and TMAs were constructed.
Immunohistochemistry (IHC) for CD10, BCL6, MUM-1, GCET1, FOXP1, and LMO2 protein expression was used to assign cell of origin (COO) by three different algorithms. IHC for MYC, BCL2, PDL-1, and HLA class II protein expression was also performed. In situ hybridization for Epstein-Barr virus-encoded RNA (EBER) was performed. Fluorescent in-situ hybridization (FISH) was performed for MYC, BCL2, BCL6, PDL1/2 (9p24.1), and CIITA (16p13) rearrangements.
Results
A total of 115 patients with PCNSL with DLBCL histology were included in the final analysis: 59% male, 70% age >60 years, 77% performance status >1. Primary treatment modalities included high-dose methotrexate (HDMTX) based regimens in 52 (45%) patients, whole brain radiotherapy (WBRT) alone in 40 (35%) patients, and best supportive care in 23 (20%) patients. Among the 52 HDMTX-treated patients, 18 also received WBRT (pre-planned combined modality therapy or inability to tolerate HDMTX), and 11 also received rituximab.
Failure of IHC/FISH occurred in 0-21% of individual assays, largely due to insufficient tissue material. The majority of patients had a non-GCB COO phenotype as determined by the Hans (76%), Choi (86%), and Tally (99%) algorithms. MYC protein expression was positive (≥40%) in 37/93 (40%) patients, BCL2 (≥50%) in 68/91 (75%) [124 antibody] and 87/111 (78%) [E17 antibody] patients, and dual MYC/BCL2 in 30/88 (35%) [124 antibody] and 32/92 (35%) [E17 antibody] patients. PDL-1 protein expression was positive (≥1%) in 31/107 (29%) patients. HLA class II antigen expression was positive (≥10%) in 75/112 (67%) patients, with staining restricted to cytoplasm (70%) or cell membrane (30%). EBER was positive (any staining) in 8/108 (7%) patients.
Chromosomal rearrangements by FISH were very uncommon for MYC 1/93 (1%), BCL2 1/110 (1%), PDL1/2 1/101 (1%), and CIITA 3/105 (3%). There were no dual rearrangements involving MYC and BCL2, although the only patient with a MYC rearrangement also had a concurrent BCL6 rearrangement. In contrast, BCL6 rearrangements were present in 33/108 (31%) patients, while BCL6 protein expression was positive in 86/111 (77%) patients.
With a median follow-up of 8 years (range 8 months - 16 years) in living patients, the 5-year PFS and OS estimates were 11% and 24%, respectively. In univariate analysis, elevated LDH, treatment with WBRT alone or supportive care, and the presence of BCL6 rearrangements (HR 1.73 [95% CI 1.12, 2.66], p=0.011) were significantly associated with worse PFS. Age >60, poor performance status, and treatment with WBRT alone or supportive care were significantly associated with worse OS, and a trend observed with the presence of BCL6 rearrangements (HR 1.46 [95% CI 0.95, 2.27], p=0.085). All other clinical and pathologic variables were not associated with PFS or OS. In the 52 patients treated with HDMTX-based regimens, the presence of a BCL6 rearrangement was the only variable associated with a worse PFS (HR 2.50 [95% CI 1.25 - 5.01], p=0.007), and no variables were associated with OS.
Discussion and Conclusions
This large TMA study shows that prominent molecular features of PCNSL are different from those of systemic DLBCL. There was a high TMA failure rate reflecting the limitations of brain biopsies, which are often stereotactic needle biopsies, small surgical samples, or obtained after a course of corticosteroids. Consistent with other reports, the majority of cases had a non-GCB phenotype by IHC algorithms, but cell of origin did not impact PFS or OS. MYC, BCL2, and PDL-1 protein expression were common but their corresponding gene rearrangements were extremely uncommon suggesting alternate mechanisms driving expression. BCL6 rearrangements were frequent and were the only factor associated with a poor prognosis in the overall cohort and in the subgroup of patients treated with HDTMX-based regimens.

Disclosures
Connors: Janssen: Research Funding; Genentech: Research Funding; NanoString Technologies: Patents & Royalties: Named Inventor on a patent licensed to NanoString Technologies, Research Funding; Merck: Research Funding; Bristol Myers-Squibb: Research Funding; Bayer Healthcare: Research Funding; F Hoffmann-La Roche: Research Funding; Roche Canada: Research Funding; Lilly: Research Funding; Seattle Genetics: Honoraria, Research Funding; Takeda: Research Funding; Amgen: Research Funding; Cephalon: Research Funding. Sehn:TG Therapeutics: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Karyopharm: Consultancy, Honoraria; Morphosys: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Abbvie: Consultancy, Honoraria; Seattle Genetics: Consultancy, Honoraria; Lundbeck: Consultancy, Honoraria; Roche/Genentech: Consultancy, Honoraria; Merck: Consultancy, Honoraria. Scott:Celgene: Consultancy, Honoraria; Janssen: Research Funding; Roche: Research Funding; NanoString: Patents & Royalties: Named Inventor on a patent licensed to NanoString Technologies, Research Funding. Steidl:Juno Therapeutics: Consultancy; Bristol-Myers Squibb: Research Funding; Tioma: Research Funding; Seattle Genetics: Consultancy; Nanostring: Patents & Royalties: patent holding; Roche: Consultancy. Gascoyne:NanoString: Patents & Royalties: Named Inventor on a patent licensed to NanoString Technologies.