Biallelic loss-of-function mutations in MAD1 result in systemic inflammation, clonal selection of aneuploid cells and high tumor susceptibility

Aneuploidy is a frequent feature of tumor cells. Yet, germline mutations leading to chromosomal instability are less frequent and are typically found in patients with mosaic variegated aneuploidy (MVA). We describe here novel germline biallelic loss-of-function mutations in MAD1L1, a gene that encodes the Spindle Assembly Checkpoint (SAC) protein MAD1, in a 36-year-old female with microcephaly and developmental delay. The patient developed a constelation of benign and malignant neoplasias derived from the three embryonic layers, some of them such as pilomatrixoma, bone tumors enchondromas and multinodular goiter rarely described in MVA. Cytogenetic and single-cell DNA analysis of peripheral blood cells detected ~35% of aneuploid cells with a variety of random gains of chromosomes. Functional studies demonstrated deficient SAC responses in the absence of MAD1 in mutant lymphocytes. Transcriptomic studies of peripheral blood cells at the single cell level suggested inhibition of protein synthesis, and increased antigen presentation and cytokine signaling in aneuploid T-cells. These pathways were also deregulated in euploid cells from the patient suggesting an immflamation-like, systemic response to chromosomal instability. In addition, single cell RNA-seq analysis detected clonal expansions affecting chromosomes 12 and 18 in specific B-cell and T-cell populations without evidence of hematopoietic neoplasias. These data point to MAD1L1 as a new gene mutated in MVA, and suggest that clonal expansion of minor aneuploid cell populations can be detected in pro-tumoral stages using single-cell technologies. Overall design: PBMCs with wild type and MAD1L1 gene mutations