Hereditary Mutations Are Present As Pathogenic or Predisposition Factors in Otherwise Typical Adult MDS

Familial MDS has been rarely reported, with few cases usually being in the context of early-onset disease and germline (GL) mutations. Patients with familial RUNX1 mutations show thrombocytopenia and progression towards MDS/AML. Similarly, germ line-(GL) CEBPA and GATA2 mutations are associated with MDS/AML. Within typical MDS, late presentation makes it difficult to distinguish hereditary factors from aging or environmental exposures. Only in rare cases, a strong family history may suggest a genetic predisposition.

Most of the NGS-based projects focused on discovery of somatic mutations, but it can ]also be used to search for disease prone GL-encoded sequence alterations. For the purpose of this study we hypothesized that in a proportion of seemingly sporadic MDS, known or new GL mutations may be present. They may predispose to disease evolution or constitute a first hit with a long latency, making assessment of penetrance difficult. Because of the tremendous amount of data generated through unbiased cross-sectional approaches and validation needed, we have devised various rational prioritization and analytic strategies: i) we stipulated that genes affected by somatic mutations may also be targets of GL alterations; ii) we screened for alterations in a panel of genes known to constitute predisposing factors to cancer and found in a limited WE NGS study (N=106) to be more frequent than expected in MDS. These genes were included in a somatic targeted panel of 81 genes.

In total we have analyzed 459 patients with typical MDS and focused on results of the above described analytic strategies. All identified alterations were independently validated to exclude somatic lesions and technical artifacts. Following sequencing, tier-1 lesions were defined as known disease-prone sequence alterations/mutations, new nonsense/frameshift mutations and highly recurrent missense mutations exceedingly rare in the general population. Tier-2 lesions were defined as missense mutations with general population frequency of <1% in the general population. Among those, the prioritization is according to the frequency and predicted impact on the protein function. For example, among tested genes, we found a total of 73 tier-1 lesions (>1) MDS. Altogether (tier-1/2) we identified 281 non-synonymous GL sequence alterations in 209 cases (45%). Surprisingly, high frequencies of mutations in DNA repair genes (including ATM, ATR or FA genes) were found in heterozygous and even (4 cases) in biallelic configuration. We also identified adult patients with otherwise typical Li-Fraumeni TP53/CHEK2 mutations. In total we found 40 tier-1 FA gene mutations, 7 ATM and 6 telomerase complex mutations and many others. One of FA genes was found to be affected by a novel, recurrent, frameshift GL variant present in 4 cases. Interestingly, the same locus is mutated in 2 non-hematological cell lines and there are proximal somatic mutations reported in that region. Several clinical and molecular associations were found when patients with various tier-1 mutations were studied. For instance, the presence of heterozygous GL mutations in FA/DNA repair genes were associated with somatic deletion of chr.7 or del5q (P<.001).

We also classified 208 tier-2 alterations. Among them, we focused our analysis on the most recurrent alterations. Not surprisingly some of the genes frequently affected by tier 1 mutations also showed common tier-2 mutations. Examples include heterozygous tier-2 genes such as, FA genes and ATM found in 9% and 14% patients, respectively. For some of the functionally related genes a combined tier-1/2 analysis was performed. For instance, analysis of telomerase machinery genes included NOP10, POT1, TERT, TERC and DKC1. Surprisingly, out of 5 different variants in TERT found in MDS patients, 2 were canonical, p.H412Y (N=3) and p.A279T (N=3) and reported to be pathogenic in hereditary aplastic anemia. Most frequent SNVs were found in ATM (N=66) and APC (N=20).

In conclusion, our results suggest that important GL alterations in cancer predisposition genes can be found in patients with otherwise seemingly sporadic MDS. Some of the genes thought to cause MDS in recessive fashion may contribute to MDS susceptibility in a delayed mode when present in heterozygous configuration. We conclude that already our very limited screen suggests inherited factors may play an important role in the pathogenesis of adult MDS.