Rare Candidate Variants for Germline Predisposition to Childhood Lymphomas: Go Beyond Aberrations in DNA Repair Genes

Introduction: Approximately 10% of pediatric patients with malignancies carry germline predisposing variants. Regarding pediatric patients who developed lymphoma, the pathogenic abnormalities frequently affect DNA repair genes. Identifying these aberrations may contribute to tailored clinical management, appropriate screening protocols, management of comorbidities, and genetic counseling. Therefore, we aimed to identify genetic predispositions to pediatric lymphoma based on familial history and phenotypical features.

Methods: We obtained clinical information about 75 patients diagnosed with lymphomas from 61 families, who met ≥1 following inclusion criteria: C1. positive familial history of cancer, C2. specific histopathological types of lymphoma, C3. multiple malignancies, C4. congenital abnormalities or specific dysfunctions, and C5. excessive toxicity of oncological treatment. Patients with known genetic diagnoses or those without consent were excluded from our study. To date, 42 families (69%), encompassing 54 patients, have been tested using next-generation sequencing (NGS): targeted panels were employed in cases with a strong clinical suspicion of a specific syndrome, while whole exome sequencing was performed in other cases. Variants were filtered based on a list of genes involved in cancer development or/in immune dysregulation using the following filters: 1) frequency below 5%; 2) at least 7 reads, 3) positive verification in Integrative Genomics Viewer. Their pathogenicity was estimated based on American College of Medical Genetics guidelines. Selected variants were then directly sequenced using Sanger methods in patients and their available relatives.

Results: Among 75 lymphoma patients (49 males, 75%) with a median age of 8.5 years (IQR: 5-13), the most commonly observed tumors included: Hodgkin lymphoma (HL; 27 patients, 36%), T-cell lymphoblastic lymphoma (T-LBL; 14 patients, 19%), and diffuse large B-cell lymphoma (DLBCL; 10 patients, 13%). The most common inclusion criteria were specific histopathological types of lymphoma, which were present in 33 (54%) families, followed by C1. (19, 31% families), C4. (19, 31% families), C3. (17, 28% families), and C5. (8, 13% families). Among C1. families, 13 cases (68%) involved both parent and child(ren), and 3 cases (16%) involved only siblings. C2. families included primarily T-LBL (10, 30% families), DLBCL (9, 27% families), and primary mediastinal B-cell lymphoma (PMBL; 6, 18% families). C3. families had leukemias in 5 (29%), central nervous system tumors in 4 (24%), and >1 lymphoma in 2 (12%) cases. C4. criterion was met due to immunodeficiency in 7 patients (37%) and polyposis in 4 patients (21%). Notably, among the 7 patients (88%) with excessive toxicities, specific types of lymphoma, mainly T-LBL, were observed.

Pathogenic, causative variants, were found in 10 families (24% of tested), the variants were particularly located in CMMRD-related genes (4 families). There were also single patients carrying pathogenic: 1) TP53 variant (NM_000546:c.155_164delAATGGTTCAC), 2) compound heterozygous ATM aberrations (NM_000051:c.434T>G & large deletion of ex40-64), 3) BLM biallelic variants (NM_000057:c.1642C>T & c.2833G>A), 4) CXCR4 defect (NM_003467:c.1012dup; het), 5) FANCM biallelic variants (NM_020937:c.1972C>T; het), and 6) CHEK2 splice-site mutation (NM_001005735:c.573+1G>A; het) In the remaining 22 families, we found variants that may possibly contribute to lymphoma development, e.g. two patients with monoallelic pathogenic variant within the BRCA1 gene (NM_007300:c.4035delA and c.3756_3759del, both het) or patient with HL and Ewing’s sarcoma, with concomitant PALB2 (NM_024675.1:c.110G>A; het); and DDX41 mutation (NM_016222:c.299-3C>T). From this group gene variant involving: LCK (NM_005356:c.1176C>G; p.Asn392Lys, het) and NTRK3 (NM_001012338:c.1745G>A; p.Arg582Gln, het) were selected as the most promising candidates for further functional tests.

Conlcusion: The implementation of the NGS approach enables the uncovering of genetic predispositions to lymphoid malignancies, particularly in patients selected based on specific clinical criteria. Germline aberrations in DNA repair genes are the most frequently found in children diagnosed with lymphomas but also, several rare aberrations affecting cancer-related genes were identified.