Abstract
Introduction: Primary immunodeficiencies (PID) are a heterogeneous group of rare genetic disorders that disrupt immunity, leading to increased risk of developing recurrent infections, autoimmune disorders, and malignancies. A previous study by Mayor et al in 2018 used existing online databases for hereditary immunodeficiencies to demonstrate significant increases in lymphoma in patients with PIDs with 8-10 fold risk. Next generation sequencing (NGS) has been increasingly used for gene identification and molecular diagnosis of PIDs. In this study, we use an NGS panel that identifies genes targeted to PID, in a cohort of patients with various lymphomas to identify potential molecular pathways that correlate between PID and lymphoma.
Methods: This single center study included 61 patients, with various types of lymphoma, or were in the process of being evaluated for one. A peripheral blood or buccal swab was obtained, and samples were analyzed through an NGS panel by Invitae, which performed sequence analysis and deletion/duplication testing of 574 genes related to primary immunodeficiency, inborn errors of immunity, and cytopenias. Data collected included lymphoma type, patient demographics, treatment regimen, outcome, and the presence or absence of reported genes on the NGS panel which also included the likelihood of pathogenicity of the gene. Descriptive statistics were obtained to enumerate common lymphomas and mutations found. Reported genes were then analyzed through institutional patient health information (PHI) sensitive artificial intelligence, to identify common pathways in which the genes act on.
Results: Across the 61 patients, the median age was 53 (range 16-88) and 56% were males (N=34). 41 patients had a diagnosis of lymphoma: 33% (N=14) with CTCL, 16% (N=7) of DLBCL, 14% (N=6) of PTCL, 7% (N=3) of HL, 9% (N=4) of FL, 12% MZL (N=5), 2% LPL (N=1), 2% ALCL (N=1). The remaining 20 cases consisted of patients who were found to have leukemia, a myeloid malignancy, or had no specific diagnosis from evaluation.
Among the 61 patients who received this NGS panel, only 2 patients - one with FL and one with DLBCL - had negative tests. Most mutations were heterozygous variants of unknown significance (VUS). There was a median number of 5 mutations per patient with a range of 0-13. However, the median was 0 with range of 0-3 for mutations that were likely pathogenic or pathogenic. NOD2 and MKL1 had a frequency of 6, and RTEL, G6PD, PRKDC, DUOX2 and LYST had a frequency of 5. We found that CTCL, DLBCL, PTCL, and HL showed recurring mutations in PGM3, NOD2, DUOX2, LYST and RTEL, and that other lymphoma subtypes did not demonstrate recurring mutations. RTEL, PRKDC and G6PD are implicated in DNA repair pathways, NOD2 and DUOX2 on NF-kB activation promoting sustained immune activation and thus lymphocyte proliferation and survival and MKL1 is involved in cytoskeletal signaling and migration in which defects may alter immune surveillance.
Discussion: The majority of lymphoma patients in our dataset harbor germline variants in genes associated with PID. The most frequently mutated genes are central to innate immunity, DNA damage repair, and cytoskeletal function, raising the hypothesis that hereditary defects in immune regulation may contribute to the development of lymphoma. This highlights the potential utility of this genomic evaluation. While most mutations were variants of unknown significance (VUS), they did lead to changes in protein and may have clinical significance that is yet to be recognized. This is a hypothesis generating project which is continuing to accumulate data, with further analysis to be done in the future with a larger patient population.
