Integration of genomics and transcriptomics allows the identification of rare DNA damage defects in PID patients with a cancer predisposition

Introduction Primary immunodeficiencies (PIDs) are a heterogeneous group of disorders caused by genetically determined defects of the immune system, predisposing to life-threatening complications such as severe and recurrent infections, auto-immunity and malignancies. A subset of PIDs is caused by pathogenic germline variants in DNA repair genes. As a consequence these patients are radiosensitive and present with increased cancer risk. Since PID patients are exposed to radiation for several reasons (bone marrow transplantation, radiotherapy, diagnostic imaging), identification of the genetic defect is important for risk stratification and improved therapeutic management. As in only 5-20% of the patients pathogenic variants are found in currently known PID genes, we hypothesize that defects in additional DNA damage response genes may be involved in PID patients prone to malignancies. We applied an integrated approach of whole exome sequencing (WES) and transcriptomics to identify the underlying genetic defect in a patient with primary dwarfism, facial dysmorphia, skeletal abnormalities, severe microcephaly, mental retardation and immunodeficiency. Materials and Methods WES data is analyzed by means of a PID gene panel (460 genes) and a DNA damage response panel consisting of >1230 genes. Extensive filtering results in a long list of variants of unknown clinical significance (VUS). To facilitate variant prioritization we are complementing WES with transcriptomics on RNA extracted from short term lymphocyte cultures. We search for expression and splicing outliers in the transcriptome. Results WES did not reveal a pathogenic variant in the PID gene panel, but a homozygous variant at position +5 in intron 5 of the DNA repair gene ATRIP was found in the patient. RNA-Seq showed skipping of exon 5, leading to a premature stop codon. This was confirmed using Sanger sequencing at the cDNA level. No full length ATRIP transcripts were detected. Additionally western blot analysis shows complete absence of ATRIP protein in our patient. Our patient only is the second ATRIP-deficient patient. The first patient ((Ogi et al. 2012)) had a clinical diagnosis of Seckel syndrome. Clinically our patient resembles SS, but additionally presents with an immunodeficiency. Previously a link between this gene and PID has not been established. Further functional validations are ongoing to provide insights into the link with the immune phenotype. Conclusions In summary, these first findings encourage the complementation of a PID gene panel with a panel of DNA damage genes for the molecular work-up of PID patients with a (presumed) cancer predisposition. Furthermore, transcriptomics allows prioritization of variants and improves diagnosis and patient management. We expanded the molecular and clinical spectrum of Seckel syndrome by describing the second ATRIP-deficient patient. Further functional work-up will contribute to the disease mechanism