Genetics of Monosomy 7 and Del(7q) in MDS Informs Potential Therapeutic Targets

Monosomy (-7) and deletions of the long arm of chromosome 7 (del7q) are frequently found in patients with myeloid neoplasms, suggesting a crucial role of this region in disease pathogenicity. -7/del7q conveys a poor prognosis and no targeted therapies exist for patients harboring this defect. We previously characterized the most common deleted regions (CDR) of del7q, including 7q22, 7q34, and 7q35-36, as well as micro deletions on del7q indicative of pathogenic genes. Unlike del5q, -7/del7q is affected both by deletions and somatic UPD, suggesting that loss of heterozygosity (LOH), rather than or in addition to haploinsufficient (HI) gene expression, may play a pathogenic role.

Previous studies identified possible driver genes contributing to the pathogenesis of -7/del7q including CUX1, EZH2, LUC7L2, MLL3, and SAMD9/9L. Some of these genes may be affected by somatic mutations in hemizygous (LUC7L2), or homozygous (EZH2) configurations while others are affected by germ line (GL) mutations wherein a disease-prone allele is eliminated upon somatic acquisition of -7/del7q. The pathogenic mechanisms driving evolution of -7/del7q neoplasms, though, have not been clarified and specific therapies similar to lenalidomide in del5q have not been developed yet. The outstanding open questions include: i) the rank of -7/del7q in the clonal hierarchy; ii) genetic predispositions to -7/del7q; iii) new important genes affected by LOH or HI; iv) genetic differences between -7 and del7q; and v) co-associated somatic hits.

We performed a complex molecular analysis of -7/del7q patients (N=316) using NGS: 67% with -7 (211/316) and 33% with del7q (105/316). First we performed analyses of clonal architecture using an allelic imbalance pipeline which facilitated reconstruction of clonal hierarchy. In 58% of patients -7/del7q was an ancestral lesion, while in 42% it was preceded by somatic hits such as TP53 (60%), IDH1/2 (30%), and DNMT3A (20%). The frequency of a chr7 abnormality as ancestral vs. secondary was no different in -7 vs. del7q.

We then studied somatic hits associated with -7/del7q. The most commonly mutated genes were TP53 (43%), TET2 (17%), DNMT3A (15%), and ASXL1 (11%) and the most frequent additional lesion was del5q (30%). About 40% of -7 and 58% of del7q occurred in the context of complex karyotype (CK). We then compared various clinical and mutational features of patients with -7 vs. del7q: -7 was significantly associated with +8 (p=.002), while del7q was associated with CK (p=.004). Isolated -7/del7q was associated with mutations in TET2 (35% vs. 10%, p<.001), DNMT3A (23% vs. 11%, p=.03), ASXL1 (18% vs. 4%, p<.001), and SETBP1 (18% vs. 3%, p<.001). -7/del7q in a CK was strongly associated with a worse prognosis (p=.003) and TP53 mutations (66% vs. 6% isolated -7/del7q, p<.001). Focusing on genes located on chr7, hemizygous mutations were found in CUX1 (2% vs. 4% heterozygous, het), EZH2 (5% vs. 5% het), and LUC7L2 (2% vs. 0.4% het). Mutated genes on -7/del7 not previously described as being associated with MDS included SDK1 (n=13), and CD36 (n=13), among others. Among our patients, 2% harbored SAMD9/9L and <1% heterozygous Fanconi Anemia Tier 1 GL mutations.

RNA-seq was used to identify HI genes in the CDR. We defined HI expression of a gene in a given patient as having expression < 25^th percentile of diploid MDS patients. Based on this criterion, 60% of genes were HI in at least half of the patients. Of known -7/del7q genes, we confirmed HI in CUX1 (79%), EZH2 (83%), LUC7L2 (63%), MLL3 (76%), SAMD9/9L (34% / 53%) among -7/del7q. Expression of AQP1, KEL, and KCNH2 fulfilled the working definition of HI in diploid cases. Out of all 358 (100%) HI genes, 75% were HI in 63%, 50% in 73%, and 25% in 89% of -7/del7q patients, a diversity that could contribute to clinical heterogeneity. We also identified genes not previously reported to be HI, including PSM2 (97%), MDH2 (92%), SSBP1 (92%), and CUL1 (91%) on 7q and SNX10 (100%) and IKZF1 (96%) on 7p.

In sum, we showed the clonal hierarchy of -7/del7q and identified a number of genes that were previously not reported to be HI in -7/del7q patients. We are evaluating expression patterns to establish a minimal expression signature of -7/del7q. Further investigation of these genes could reveal their pathogenesis in myeloid disease. Other contributions from our group (V Adema et al, ASH2019) include implication of IKZF1 and CUL1 as potential drug targets in -7/del7q.