Identification of genomic biomarkers of disease progression and survival in primary CNS lymphoma

The determination of the genetic subtypes of primary central nervous system lymphoma (PCNSL) and their relationship to differential chemoimmunotherapeutic response has not been established. There is a particular need for genomic biomarkers that identify patients with newly diagnosed PCNSL at high risk of early progression and death. We applied targeted next-generation sequencing for detection of recurrent single-nucleotide variants, copy number alterations, and zygosity abnormalities in diagnostic specimens from 78 patients with PCNSL treated with a standard methotrexate-based regimen, to identify prognostically significant molecular subgroups. All patients received induction immunochemotherapy, and 44 proceeded to dose-intensive consolidation. Genomic aberrations at 4 loci were associated with 91% of lymphoma progression events and all 15 deaths: (1) chromosome 6p copy-neutral loss of heterozygosity (CN-LOH) or focal homozygous deletion (HD) at 6p21.3, and mutations of tumor suppressor genes (2) BTG1, (3) ETV6, and (4) TP53. Cox regression multivariate analysis demonstrated a high risk of progression in patients with aberrations at these loci. Genomic aberrations at these loci were also associated with significantly shorter survival. Lower expression of HLA-DR was associated with 6p CN-LOH/6p21.3 HD and inferior prognosis. These genomic aberrations identify a high-risk molecular subgroup that may inform risk stratification in PCNSL. Further elucidation of the mechanisms of therapeutic resistance associated with the high-risk genetic phenotype is requisite to facilitate precision medicine and progress in therapy.