Germline TET2 loss of function causes childhood immunodeficiency and lymphoma

Molecular dissection of inborn errors of immunity can help to elucidate the nonredundant functions of individual genes. We studied three children with an immunodysregulatory syndrome of susceptibility to infection, lymphadenopathy, hepatosplenomegaly, developmental delay, autoimmunity and lymphoma of either B- (n=2) or T-cell (n=1) origin. All three showed early autologous T-cell reconstitution following allogeneic hematopoietic stem cell transplantation. By whole exome sequencing, we identified rare, homozygous, germline missense or nonsense variants in a known epigenetic regulator of gene expression, Ten-Eleven Translocation methylcytosine dioxygenase 2 (TET2). Mutated TET2 protein was either absent or enzymatically defective for 5-hydroxymethylating activity, resulting in whole blood DNA hypermethylation. Circulating T-cells showed an abnormal immunophenotype including expanded double-negative but depleted follicular helper T-cell compartments, and impaired Fas-dependent apoptosis in 2/3 patients. Moreover, TET2 deficientB-cells showed defective class-switch recombination. The hematopoietic potential of patient-derived induced-pluripotent stem cells was skewed towards the myeloid lineage. These are the first reported cases of autosomal recessive germline TET2 deficiency in humans, causing clinically significant immunodeficiency and an autoimmune lymphoproliferative syndrome with marked predisposition to lymphoma. This disease phenotype demonstrates the broad role of TET2 within the human immune system.