Trisomy-6: The Ying and Yang of Chromosome 6 Aberrations

Karyotypic aberrations of chromosome 6 (chr.6), include duplications (trisomy 6; +6), deletion of its short arm (del6p), uniparental disomy 6 (UPD6p), as well as various microduplications and microdeletions. Among many important genes, the HLA locus is located on 6p, and loss of heterozygosity and allelic loss have been described as means of immune escape in immune-mediated aplastic anemia (AA) and in relapse of myeloid neoplasia following allogeneic bone marrow transplant. The pathogenesis of duplication of chr.6 appears more complex and might involve deletion of a putative tumor suppressor gene (TSG) causing duplication of the HLA locus with increased HLA expression.

We have encountered several patients with +6 who inspired us to investigate the clinical and molecular phenotypes of +6. A total of 29 +6 MDS patients were identified, of whom 16 had isolated +6 (Iso +6). When compared to normal karyotype (NK) MDS (n=420), median age was younger in Iso +6 (70 vs 42 years, P<.0001). While no differences were noted for white blood counts, Iso +6 patients had lower platelets (median 27 vs. 112 x 10³/uL, P=.19), were more frequently anemic (median hemoglobin 8.4 vs. 9.5 g/dL, P=.04) and showed higher frequency of hypocellularity at marrow evaluation (62.5% vs. 9.5%, P=0.0016) as opposed to NK MDS. Indeed, 67% of Iso +6 patients had a clinical picture reminiscent of AA or MDS phenotype which might have evolved from an antecedent AA phase. However, 67% of Iso +6 MDS had high risk MDS (IPSS-R ≥3.5) and 37% transformed to AML. Thus, our cohort indicated a phenotypic dichotomy which include hypocellular MDS/AA and high-risk disease with a poor prognosis. Of all +6 MDS, mutations most commonly affected TP53 (69%) followed by EZH2 (19%).

Recurrent copy number variations (CNV) such as micro-duplications and microdeletions may be used to identify culprit genes. Indeed, microdeletions involving HLA have previously hinted towards the pathogenic role of HLA deletions. We obtained CNV data and compared them to conventional germline chromosome 6 CNV gains publicly available in the Database of Genomic Variants (DGV). Genes pertaining to significantly duplicated segments were then identified using the UCSC Genome Browser (https://genome.ucsc.edu/cgi-bin/hgGateway). In our cohort, in addition to 833 cases with del6p, we have identified microduplications involving 6p locus in 115 (11.5%) NK MDS cases. Overall, a total of 1198 6p copy gains were found in these patients, ranging in size 0.09-7.8Mb and with a median of 0.12Mb. The genomic architecture of each segment was investigated using the UCSC Genome Browser, from which only complete gene duplications that mirror an extra chromosomal copy were considered. Complete duplications were most commonly seen in loci containing genes of DUSP22 (12.2%) and most importantly HLA-DRB1 (10.4%), HLA-DRB5 (10.4%), HLA-DQA1 (9.6%) and MICA (9.6%). All of these five genes were significantly enriched in NK MDS as compared to healthy controls (DUSP22 3% P<0.0001, HLA-DRB1 0.4% P<0.0001, HLA-DRB5 0.5% P<0.0001, HLA-DQA1 0.5% P<0.0001 and MICA 0.2% P<0.0001) (Fig 1). Interestingly, while checking the Cosmic Cancer Browser database (https://cancer.sanger.ac.uk), we noticed that copy gains involving HLA-DRB1 and HLA-DRB5 were also more common in primary AML than in healthy controls from DGV (3.6 vs 0.4%, P<0.0001 and 3.6 vs 0.5%, P<0.0001, respectively). While the involvement of the HLA genes hints towards an immune-mediated mechanism underlying the pathogenesis of +6 MDS, further involvement in primary AML may suggest a common mechanism through which CN gains of the HLA locus promote myelo-neoplasia.

We stipulate that while clonal deletion or UPD of HLA locus can be a result of immune pressure as seen in AA and during GvL, clonal duplication may lead to increased autoantigens presentation beyond the TCR activation threshold, triggering immune reactions ultimately resulting in hypocellular marrow and AA-like presentation. Alternatively, +6 and related lesions may lead to risk allele duplication and consequential more efficient presentation of a specific antigenic peptide. In more advanced diseases, deletion of TSG may also play a role, with progression reflecting a somatic pressure to overcome immune inhibition. HLA constellation and mutational studies will be presented in the context of the findings of 6p duplications and microdeletion in MDS and AA.

Meggendorfer:MLL Munich Leukemia Laboratory: Current Employment. Haferlach:Munich Leukemia Laboratory: Current Employment, Other: Part ownership. Maciejewski:Alexion: Consultancy; Apellis Pharmaceuticals: Consultancy.