Somatic Mutations and Loss-Of-Heterozygosity Impair The DNA Repair Functions Of CUX1 in Myelodysplastic Syndromes (MDS)

Chromosome 7 lesions are common and are associated almost uniformly with a deleterious outcome in MDS and related myeloid neoplasms. We analyzed a large cohort of these patients (pts) (n=1595) and identified those with loss of heterozygosity (LOH) of chromosome 7, including del(7q), monosomy7 (-7) and UPD(7q) in 171 cases. Using single nucleotide polymorphism (SNP)-array karyotyping, 3 commonly deleted regions (CDR) have been isolated, including 7q22, 7q34, and 7q35-36. CDR 7q22 was involved in 119 cases and spanned among others PLOD3, RBL5 and CUX1 genes, which could play a role in del(7q) pathogenesis. To further investigate the molecular pathogenesis of -7/del(7q), we performed whole exome new generation sequencing (NGS) in 428 pts with MDS and related conditions; this cohort included 72 -7/del(7q) or UPD7. When we studied the mutational status of genes in 7q22, we noted 5 cases of CUX1mutations, including 2 with heterozygous and 3 with homozygous mutations (associated with UPD7q).

These mutations were validated by Sanger sequencing and targeted deep sequencing of DNA from both tumor and normal cells. All CUX1 mutations revealed critical structural and functional determinants such as nonsense mutations resulting in premature stop codons (n=3), nonsense mutation located in the DNA-binding Cut homeodomain (p.R1296K, n=1) and splice site mutation (n=1). CUX1 mutation occurred in MDS (n=2) and MDS/MPN (n=3), and concomitant TET2 mutations were seen in 4 cases. No hemizygous CUX1mutations were found in cases with del(7q).

CUX1 is haploinsufficient in cases with -7/del(7q). In total 166 cases (10.9%) had -7/del(7q) involving CUX1, in addition to pts in whom CUX1 was affected by likely hypomorphic/inactivating mutations. Pts with decreased expression of CUX1 had poor survival compared to pts without CUX1 (p<.01, HR=1.99), suggesting that deficient function (deletion or mutation) of CUX1affects disease progression.

In addition to somatic mutations, LOH of CUX1 has been reported in several cancers. A role of CUX1 as a haploinsufficient tumor suppressor cannot be explained by the known functions of CUX1 in stimulating cell proliferation, motility and resistance to apoptosis. We recently identified a novel molecular function of CUX1 in DNA repair that may explain how haplo-deficient expression of CUX1 contributes to leukemic transformation. We used single cell gel electrophoresis (comet assay) to show that Cux1^-/- mouse embryo fibroblasts (MEFs) are deficient, while Cux1^+/- MEFs are haploinsufficient, in the repair of oxidative DNA damage. Using an inverse-PCR assay, following etoposide exposure, the frequency of chromosomal translocations involving the mixed lineage leukemia (Mll) gene is significantly and progressively increased in Cux1^+/- and Cux1^-/- MEFs compared to Cux1^+/+ MEFs. We then performed comet assays using primary leukemic cells that harbor a frameshift mutation predicted to inactivate CUX1 by producing a C-terminally truncated protein devoid of a nuclear localization signal. Repair of oxidative DNA damage was delayed in leukemic cells compared to bone marrow cells from a healthy donor. Using an in vitrobase excision repair assay, we show that repair of 8-oxoguanine is reduced in a cell line displaying LOH of CUX1. Similarly, repair of 8-oxoguanine is reduced following siRNA-mediated CUX1 knockdown, but is rescued by the addition of a purified CUX1 protein. Together these results demonstrate that CUX1 plays a direct role in DNA repair and that inactivation of one CUX1 allele reduces the DNA repair capability of cells.

In conclusion, novel somatic mutations of CUX1 as a candidate gene are associated with poor prognosis in MDS pts with -7/del(7q) and UPD7. Somatic events constitute loss of function of CUX1, resulting in insufficiency of DNA repair mechanisms, which is associated with leukemogenesis and could be considered as a new therapeutic target. CUX1 mutations may affect base excision repair, and dysfunction of CUX1 could theoretically predispose to chromosomal translocations and complex karyotype, seen in conjunction with del(7q) cases.