Geno-Transcriptomic Topography of Clonal Drivers in Trisomy 8 Myeloid Malignancies

Trisomy 8 (+8) is a frequent cytogenetic aberration occurring in various types of myeloid neoplasia (MN). The prognostic impact of +8 is disease context-dependent as is reflected by its divergent clinical consequences resulting in its categorization as an intermediate risk cytogenetic abnormality in AML (per 2022 ELN recommendations) vs being less detrimental in MDS in IPSSR. To date, the intrinsic molecular culprits driving the clonal pathogenesis of +8 MN are not entirely known. We conducted an integrative data analysis of +8 MDS and AML to elucidate its unique clinical, genomic, and transcriptomic features and narrowed the search for genetic drivers or therapeutic targets. We analysed clinical and molecular features of MDS (n=3588) and AML (n=6788) cases (from internal and publicly available sources) to identify +8 cases and then collated clinical annotations to establish genotype-phenotype associations. NGS based expression analysis was performed on a subset of these cases. We identified 641 +8 AML patients, including 294 isolated (iso) +8 and 347 non-iso +8 AML cases. Iso +8 AML had higher percentages of sAML (17%) vs NK AML (11%, P=.001). +8 patients presented with a hyper dysplastic phenotype having lower white blood cells (median: 8.6 vs 14.4 x109/L, P= .02) and platelet counts (median: 47.5 vs 63.0 x109/L, P= .01). Iso +8 AML had worse median overall survival (mOS) compared to patients with NK AML (n=275 vs 3276; 20 vs 32 mo., P<.0001). When sub-stratified, iso +8 cohort vs NK AML according to primary vs secondary ontogeny, a significant difference in mOS was exclusively seen in pAML (21.5 vs 34.5 mo., P=0.0002) while no difference was seen in sAML (15 vs 24 mo., P=.32). We then studied the molecular associations of +8 AML and identified a signature of mutations that was more enriched in iso +8 AML vs NK AML including lineage transcriptional factors (RUNX1, 33 vs 17%, P< .0001), chromatin modifiers (ASXL1, 37 vs 13%, P<.0001; EZH2, 10 vs 3%, P< .0001), splicing factors (SRSF2, 30 vs 14%, P< .0001; U2AF1, 13 vs 3%, P<.0001), metabolic enzymes (IDH2, 25 vs 19%, P= .04), and cohesin genes (STAG2, 13 vs 7%, P= .02). We then focused on the iso +8 MDS vs NK MDS groups, and interestingly, found that ASXL1 (48 vs 19%, P<.0001), EZH2 (19 vs 3% P<.0001), RUNX1 (31 vs 12%, P= .0002), and STAG2 (26 vs 6%, P<.0001) were more frequently found in +8 MDS compared to NK MDS (in a similar patten to iso +8 AML vs NK AML). The comparison of AML and MDS then showed that iso +8 AML was more commonly associated with mutations in FLT3 (32 vs 5%, P<.0001), IDH1 (17 vs 4%, P=.0077), and IDH2 (25 vs 7%, P=.0016), while iso +8 MDS had higher odds of SF3B1 (19 vs 4%, P= .0008) and STAG2 (26 vs 13%, P=.04). In terms of transcriptomic profile, we then investigated the specific RNA expression changes potentially implicated in the pathogenesis of +8 MN to identify an imbalance between changes in oncogenes vs tumor suppressor genes (TSG). Thus, we targeted the transcriptome of 412 genes mapping on chr8 in 46 +8 MDS and 502 NK MDS patients. We identified 186 genes of which a change in mRNA expression levels was significantly correlated with clonality. We further interrogated these genes for the possibility of eliciting oncogenic potential by estimation of the log2 fold change (log2FC) in expression ratio (compared to NK disease) of at least 1.25 to reflect an extra chr8 copy. We found consistently higher mRNA expression levels of 5 putative culprit genes of known transforming oncogenes in iso +8 MDS vs. NK MDS including the antiapoptotic protein BAG4 (logFC 7.1 vs 5.4, P=.0001), possibly conferring growth advantage, toll-like receptor LY96 (logFC 3.3 vs 2.0, P=.0001), the tyrosine protein kinase LYN (logFC 8.4 vs 6.7, P=.0001), human oncogene WHSC1L1/NSD3 (logFC 8.1 vs 6.5, P=.0001) and long non-coding RNA, PVT1 derived from an 8q24 intergenic region (logFC 4.0 vs 2.2, P=.0001). No significant differences and clonality correlation were noted in the expression of putative chr8 TSG. Literature search reconciled experimental data supporting an oncogenic role of the aforementioned genes located in the amplified 8p11-p12 region for whom small molecule inhibitors are available. In summary, the key clonal drives implicated in +8 MN may be located on the extra chr8 itself. Indeed, we found transcriptomic changes in oncogenes pertinent to +8 MDS whose interaction with specific myeloid drivers could enlighten on therapeutic prospectives.